Methods for high fidelity production of long nucleic acid molecules with error control

ABSTRACT

This invention generally relates to nucleic acid synthesis, in particular DNA synthesis. More particularly, the invention relates to the production of long nucleic acid molecules with precise user control over sequence content. This invention also relates to the prevention and/or removal of errors within nucleic acid molecules.

CROSS-REFERENCE TO RELATED PATENT APPLICATIONS

This application is related to the copending application titled “Methodsfor High Fidelity Production of Long Nucleic Acid Molecules” by Carr etal., U.S. patent application Ser. No. 10/733,847, filed concurrentlyherewith on Dec. 10, 2003.

This application is a an application claiming the benefit under 35 USC119(e) U.S. Application 60/432,556, filed Dec. 10, 2002, incorporatedherein by reference in its entirety.

FIELD OF THE INVENTION

This invention generally relates to nucleic acid synthesis, inparticular DNA synthesis. More particularly, the invention relates tothe production of long nucleic acid molecules with precise user controlover sequence content. This invention also relates to the preventionand/or removal of errors within nucleic acid molecules.

BACKGROUND OF THE INVENTION

The availability of synthetic DNA sequences has fueled major revolutionsin genetic engineering and the understanding of human genes, makingpossible such techniques as site-directed mutagenesis, the polymerasechain reaction (PCR), high-throughput DNA sequencing, gene synthesis,and gene expression analysis using DNA microarrays.

DNA produced from a user-specified sequence is typically synthesizedchemically in the form of short oligonucleotides, often ranging inlength from 20 to 70 bases. For methods and materials known in the artrelated to the chemical synthesis of nucleic acids see, e.g., Beaucage,S. L., Caruthers, M. H., The Chemical Synthesis of DNA/RNA, which ishereby incorporated by reference. Syntheses of longer oligonucleotidesare possible, but the intrinsic error rate of each coupling step(typically 1-2%) is such that preparations of longer oligonucleotidesare increasingly likely to be riddled with errors, and that the puredesired product will be numerically overwhelmed by sequences containingerrors. Thus to produce longer DNA sequences, the molecule is notsynthesized as a single long piece. Rather, current methods involvecombining many shorter oligonucleotides to build the larger desiredsequence, a process often referred to as “gene synthesis” (though theproduct need not be confined to a single gene).

Linear synthesis of nucleic acids may be accomplished using biologicalmolecules and protecting groups. The most common linear synthesistechniques are based on solid-phase phosphoramidite chemistry. The3′-phosphate is affixed to solid-phase support (typicallycontrolled-pore glass beads, silicon substrates, or glass substrates),and an individual nucleotide of choice is added to a chain growing inthe 3′-5′ direction by means of a 5′-protecting group (typically anacid-labile or photo-cleavable protecting group). In linear synthesesbased on phosphoramidite chemistry, there are many potential sources ofsequence error and oligonucleotide damage that are well documented. Mostnotably, the removal of the 5′-protecting group usually involves anacidic treatment that can remove the base, or in the case ofphoto-labile 5′-protecting group, require ultraviolet irradiation thatcan damage the nucleotide. The nucleotide may fail to incorporate intothe growing strand because of insufficient reaction time. Nearly allorganic and inorganic solvents and reagents employed in the process canchemically damage the growing nucleotide. Such sources of errorultimately limit the fidelity and length of the oligonucleotide, andfurthermore, limit the fidelity and length of larger nucleic acidsassembled from linearly synthesized strands. For methods and materialsknown in the art related to phosphoramidite nucleic acid synthesis see,e.g., Sierzchala, A. B., Dellinger, D. J., Betley, J. R., Wyrzykiewicz,Yamada, C. M., Caruthers, M. H., Solid-Phase OligodeoxynucleotideSynthesis: A Two-Step Cycle Using Peroxy Anion Deprotection, J. AM.CHEM. SOC., 125, 13427-13441 (2003), which is hereby incorporated byreference.

Errors in gene synthesis are typically controlled in two ways: 1) theindividual oligonucleotides can each be purified to remove errorsequences; 2) the final cloned products are sequenced to discover iferrors are present. In this latter case, the errors are dealt with byeither sequencing many clones until an error-free sequence is found,using mutagenesis to specifically fix an error, or choosing andcombining specific error-free sub-sequences to build an error free fulllength sequence.

Synthesizing a single gene has become commonplace enough that manycompanies exist to perform this task for a researcher. Single genes upto about 1000 base pairs (bp) are typically offered, and largersequences are feasible, up to about 10,000 bp, for the construction of asingle large gene, or a set of genes together. A recent benchmark wasthe production of the entire poliovirus genome, 7500 bp, capable ofproducing functional viral particles. These syntheses of long DNAproducts employ the methods described above, often aided by thelarge-scale production of oligonucleotides, such as with mutiplexed 48-,96- or 384-column synthesizers, and using sample-handling robots tospeed manipulations. For methods and materials known in the art relatedto gene synthesis, see e.g., Au., L., Yang, W., Lo., S., Kao, C., GeneSynthesis by a LCR-Based Approach: High-Level Production of Leptin-L45Using Synthetic Gene in Escherichia Coli, BIOCHEM. & BIOPHYS. RESEARCHCOMM., 248, 200-203 (1998); Baedeker, M., Schulz, G. E., Overexpressionof a Designed 2.2 kb Gene of Eukaryotic Phenylalanine Ammonia-Lyase inEscherichia coli, FEBS LETTERS 475, 57-60 (1999), Casimiro, D. R.,Wright, P. E., Dyson, H. J., PCR-based Gene Synthesis and Protein NMRSpectroscopy, STRUCTURE, Vol. 5, No. 11, 1407-1412 (1997); Cello, J.,Paul, A. V., Wimmer, E., Chemical Synthesis of Poliovirus cDNA:Generation of Infectious Virus in the Absence of Natural Template,SCIENCE, 297, 1016-1018 (2002); Kneidinger, B., Graninger, M., Messner,P., Scaling Up the Ligase Chain Reaction-Based Approach to GeneSynthesis, BIOTECHNIQUES, 30, 249-252 (2001); Dietrich, R., Wirsching,F., Opitz, T., Schwienhorst, A., Gene Assembly Based on Blunt-EndedDouble-Stranded DNA-Molecules, BIOTECH. TECHNIQUES, Vol. 12, No. 1,49-54 (1998); Hoover, D. M., Lubkowski, J., DNAWorks: An AutomatedMethod for Designing Oligonucleotides for PCR-based Gene Synthesis,NUCLEIC ACIDS RESEARCH, Vol. 30, No. 10, 1-7 (2002); Stemmer, W. P. C.,Crameri, A., Ha, K. D., Brennan, T. M., Heyneker, H. L., Single-StepAssembly of a Gene and Entire Plasmid from Large Numbers ofOligodeoxyribonucleotides, GENE, 164, 49-53 (1995); Withers-Martinez,C., Carpenter, E. P., Hackett, F., Ely, B., Sajid, M., Grainger, M.,Blackman, M. J., PCR-Based Gene Synthesis as an Efficient Approach forExpression of the A+T-Rich Malaria Genome, PROTEIN ENG., Vol. 12, No.12, 1113-1120 (1999); and Venter Cooks Up a Synthetic Genome in RecordTime, SCIENCE, 302, 1307 (2003) all of which are hereby incorporated byreference. For patents and patent applications related to genesynthesis, see e.g., U.S. Pat. Nos. 6,521,453 and 6,521,427, and U.S.Pat. App. Pub. Nos. 20030165946, 20030138782, and 20030087238, allhereby incorporated by reference.

As the goals of genetic engineers become more complex and larger inscale, these methods become prohibitive in terms of the cost, time, andeffort involved to produce longer sequences and correct the subsequenterrors. For example, a fee may be $5 per bp for a 500 bp sequence, witha waiting time of 2-4 weeks, whereas even the most rapid portion of thepoliovirus synthesis required several months and tens of thousands ofdollars (the project overall required two years and over $100,000). Atechnology which makes this process both faster and more affordablewould be a tremendous aid to researchers in need of very long DNAmolecules.

Some examples of work which would benefit:v

1) Vaccine trials (modest DNA length, but many variants): in producingproteins for use in vaccine trials, a large number of variant proteinsequences are often examined. The number of options explored istypically limited by the number of variants that can be produced. Thelengths of the DNA molecules encoding such proteins might be in therange of about 100 bp to about 2000 bp, or longer, depending on theprotein. One of ordinary skill in the art will understand that thelength of a DNA molecule may vary greatly depending on the proteinproduct desired.

2) Gene therapy (intermediate DNA length): retroviral vectors used forgene therapy might range from about 20,000 to about 50,000 bp. Theprocess of constructing these vectors also limits the number andcomplexity of variants which can be tested in the laboratory.

3) Bacterial engineering (greatest DNA length, genomic synthesis):currently, changes made to a bacterial organism are attempted one geneat a time, a painstaking process when several changes are desired. Inthe case of engineering a bacterium to perform a task, such as wastedetoxification or protein production, a large number of intricatechanges may be required. If the complete genome of the desired bacteriumcould be generated easily de novo, a great deal of time and effort couldbe saved, and new areas of research would be made possible. Bacterialgenomes range from several hundred kilobases to many megabases. One ofordinary skill in the art will understand that the size of bacterialgenomes varies greatly depending on the bacterium in question.

The fundamental challenges of the current technology:

1) Scaling: as the size of the desired sequence grows, the productiontime and costs involved grow linearly, or worse. An ideal method wouldinvolve smaller amounts of reagents, shorter cycle times foroligonucleotide synthesis, a greatly improved parallelization of thesynthesis process used to provide the oligonucleotides, and/or animproved process for the assembly of oligonucleotides into largermolecules.

2) Errors: with the production of larger DNA sequences, expected perbase error rates will essentially guarantee that conventional methodswill yield sequences containing errors. These errors will require moreeffective techniques than the current control procedures describedabove.

SUMMARY OF THE INVENTION

The present invention provides methods for the error-free production oflong nucleic acid molecules with precise user control over sequencecontent. In a preferred embodiment of the invention, long error-freenucleic acid molecules can be generated in parallel fromoligonucleotides immobilized on a surface, such as an oligonucleotidemicroarray. The movement of the growing nucleic acid molecule can becontrolled through the stepwise repositioning of the growing molecule.Stepwise repositioning refers to the position of the growing molecule asit interacts with the oligonucleotides immobilized on the surface. Oneaspect of the invention allows for the synthesis of nucleic acids in aparallel format through the use of a ligase or polymerase reaction. Inanother aspect of the invention, the oligonucleotides may also bedetached from their support and manipulated by, for example, amicrofluidic device for the purpose of assembly into larger molecules.Regarding parallel DNA arrays, it is important to note that a singlenucleotide may be synthesized using the parallel arrays, and thenamplified by techniques well known in the art, such as but not limitedto, polymerase chain reaction.

In another aspect of the invention, the synthesis of a long nucleotidechain may be accomplished in parallel starting from a set of manyredundantly overlapped oligonucleotides. Synthesis relies on annealingcomplementary pairs of oligonucleotides and extending them to producelonger oligonucleotide segments, until the full-length sequence isproduced. The majority of the oligonucleotide sequence is used togenerate the complementary overlap, improving the chance of the twostrands annealing. This approach guards against the failed synthesis ofany one distinct oligonucleotide sequence, as a less complementary pairof oligonucleotides may still anneal under the appropriate conditionsand produce a full length nucleotide sequence. In another aspect of theinvention, long nucleotide sequences may contain one or more regionscontaining sites specifically designed to facilitate the joining ofseparate molecules. These sequences can be sites for specificendonuclease restriction and subsequent ligation, homologousrecombination, site-specific recombination, or transposition.

A preferred embodiment of the invention provides a method for thesynthesis of single-stranded DNA with various 3′-phosphate protectinggroups, such as but not limited to, peptide, carbohydrate, diphosphate,or phosphate derivative 3′-phosphate protecting groups. After anaddition to the nascent DNA strand by a capped nucleotide oroligonucleotide, a protease or phosphotase cleaves the bond between thecapping group and the most recently added nucleotide. DNA polymerase ornucleotide ligase can be used to add a 3′ capped nucleotide oroligonucleotide to the 3′ end of the nascent strand. DNA ligase can alsobe used to add a 5′ capped nucleotide or oligonucleotide to the 5′ endof the nascent strand.

Another preferred embodiment of the invention provides a method for thesynthesis of a double-stranded DNA with an oligonucleotides cappinggroup. The capping group is comprised of a nucleotide or shortoligonucleotide that can be cleaved from the nascent strand by arestriction enzyme. After the addition of a capped nucleotide oroligonucleotide, a restriction enzyme which recognizes the cappingnucleotide sequence will cleave the fragment 3′ to the newly addednucleotide. Thus, the desired nucleotide will remain on the nascentstrand. This procedure is repeated to create a specific oligonucleotidesequence. Different restriction enzymes and corresponding cappingnucleotides or sequence redesign may be required for the creation ofdesired oligonucleotides in order to prevent sequence recognition in thenascent strand.

Yet another preferred embodiment of the invention provides a method forthe synthesis of single-stranded and/or double-stranded DNA usingoligonucleotide hairpin-loops as heat-removable protecting groups and/orPCR primers. Oligonucleotides with secondary conformational structures,such as DNA hairpin-loops (also termed stem-loops, and molecularbeacons), can also be used as protecting groups. Gentle heating is animproved method of deprotection over enzymatic removal because heatdistributes more quickly and uniformly than enzymes because theenzymatic removal rate is diffusion-limited, and gentle heating is alower-cost resource than restriction enzymes.

The present invention also provides methods for detecting and correctingerrors that arise in the process of constructing long nucleic acidmolecules. A preferred embodiment of the invention utilizes aforce-feedback system using magnetic and/or optical tweezers, eitherseparately or in combination. Using this system, double orsingle-stranded DNA is grown off a solid-phase support using one or acombination of the aforementioned DNA synthesis methods. The solid-phasesupport is magnetic in nature and held in a fixed equilibrium positionby applying an electric field and magnetic field gradient created by themagnetic tweezers that opposes the electrophoretic force. Asoligonucleotides are annealed to the growing strand, the negativelycharged phosphate backbone adds charge to the bead-strand complex.However, the added oligonucleotide adds essentially no mass or surfacearea to the complex. Assuming the zeta-potential of the dielectric beadis constant, the addition of an oligonucleotide strand is the onlycontribution to the increase in electrophoretic force felt by theparticle. The increased electrophoretic moves the bead from itsequilibrium position, and the magnetic field gradient must be increasedto restore the bead to its equilibrium position. Optically determinedbead velocity and restoration force correspond to the number of basesadded. Therefore, the length of the added strand can be ensured to becorrect. Optical detection can be by way of a CCD or split-photodiode.This scheme in can also be modified to employ optical tweezers to applyan optical force rather than a magnetic force. Furthermore, this methodcan utilize coupled magneto-optical tweezers. The optical and magneticforces can be created simultaneously or independently of one another.

Another preferred embodiment of the invention also provides methods fordetecting and correcting errors that arise in the process ofconstructing long nucleic acid molecules. A preferred embodiment of theinvention utilizes electrophoresis as a force-feedback system. In thisscheme, a single strand of DNA is synthesized on a fluorescent beadfunctionalized with a single phosphate group, and electrophoreticallypassed through a medium with excess ATP, kinase, and ligase. The rate ofmotion of the bead is monitored and used as the feedback mechanism.First, excess ATP is passed through the medium simultaneously (with thebead). Excess ATP will pass through the medium much faster than thebead. The kinase will catalyze the formation of a triphosphate on thebead using ATP. When this occurs, the rate of motion of the bead willchange, due to a change in the charge/mass ratio. The measurement ofthis change thus serves to indicate a successful reaction. Once thetriphosphate has formed on the bead, excess free nucleotide is passedthrough the medium. These small molecules will pass through the mediummuch faster than the bead. DNA ligase will catalyze the addition of thenucleotide, releasing a diphosphate. The rate of motion of the bead isreduced because the loss of the diphosphate decreases the charge/massratio. This serves as feedback for base addition. Multiple-nucleotideaddition in this step should not occur because after one addition, thereis no triphosphate present in the system, which DNA ligase needs to addthe base. Once a successful nucleotide addition is detected, more ATP isintroduced into the system and the described cycle repeats.

Another preferred embodiment of the invention uses heat as an additionalfeedback and error correction mechanism in force feedback systems. Priorto enzymatic ligation, the melting point of the small oligonucleotide incontact with the growing nucleic acid strand will be lowered ifbase-pair mismatches occur. The controlled application of heat afterdetected annealing can provide additional feedback about base-pairmismatches. If the oligonucleotide dehybridizes from the growing strandas the melting point is approached, but not reached, a base-pairmismatch is detected when a decrease in magnetophoretic force, orincrease in electrophoretic force is required to keep the bead inequilibrium. Because the erroneous strand is removed by heat, thisfeedback process is also an error-correction mechanism.

Another preferred embodiment of the invention utilizes exonucleaseactivity for nucleotide removal for error-correction in force-feedbacksystems. This type of error-correction is particular useful forcorrecting errors after enzymatic ligation of an erroneous strand.Whereas it would be extremely difficult to control the exact number ofnucleotides that exonuclease removes from the 3′-end of a growing strandof nucleic acid, that level of control is not required in the methodsreported herein because the feedback systems allow for the length of thestrand to be determined after the error-correction steps. Therefore, iftoo many nucleotides are initially removed, they may be added backlater.

A novel aspect of the invention accounts for the potential that an errormay occur that cannot be detected or corrected by the use of paralleldetection. The parallelization of single-molecule systems is desirableto ensure that the process is successful and also allows for variousnucleic acids of different sequences to be synthesized simultaneously.Parallel single-molecule systems may use arrays of light sources anddetectors. Parallel single-molecule systems using only one light sourceand detector are also possible.

Parallel detection may also be performed without the use of arrays.Single-molecule systems in which the solid-phase supports havenegligible interactions can be parallelized without the use of arrays.For example, optical tweezers may be employed in the single-moleculesystem as described in FIG. 9B. Multiple beads in the same microscopefield of view are trapped by rastering the laser beam using anacoustical-optical modulator (AOM). In another example, multiple beadsmay be tracked using only one CCD camera. The ability to control beadsindependently is not available in this system. However, beads witherroneous nucleic acids can be tracked and discarded after the entireprocess is complete.

Another novel aspect of this invention provides methods for themicrofabrication of electromagnet arrays. The area density ofelectromagnet arrays is maximized if the electromagnets are fabricatedby bulk-microfabrication techniques. First, a layer of diagonal metalwires are lithographically defined and deposited on a silicon substrate.Bond pads are also defined in this first step. Then, a film of softmagnetic material is lithographically designed and deposited over aportion of the metal lines. A second layer of metal lines arelithographically defined and deposited over the magnetic film layer tocomplete the microfabrication of in-plane microelectromagnets.

A preferred embodiment of the invention provides a method for errordetection and correction using a nanopore device for single-moleculesynthesis with feedback using fluorescent 5′ protecting groups. DNA issynthesized on a non-fluorescent solid support and passes through asub-micron size opening, known as a nanopore, with a fluorescencedetector. The bead can be directed to one of two channels by a switch,depending on whether a successful addition has occurred. After thecoupling step and removal of excess reagents, the bead is passed throughthe pore. If no fluorescence is detected, either the coupling reactionwas unsuccessful, or it was successful but not detected. The bead isdirected back into the device for another coupling step. Because the 5′end of the growing strand is protected, a redundant coupling step willnot result in multiple-base addition.

Another preferred embodiment of the invention provides a method forerror detection and correction using uses a nanopore device forsingle-molecule synthesis with feedback using fluorescent 5′ protectinggroups. Monitoring the deprotection of the 5′ group is necessary toeliminate deletion errors. In this device, the growing strand isdeprotected, and the wash is flowed through the nanopore, not the bead,and the nanopore only leads to one channel. If no fluorescence isdetected in the wash, then the strand was not deprotected, or it wassuccessfully deprotected but the fluorescent protecting group was notdetected. The wash is constantly recycled until a fluorescent group isdetected. Because there are no free nucleotides (only the growingstrand) in this device, no addition error can occur by redundant 5′deprotection steps.

A novel aspect of the invention allows for independent control of acluster of superparamagnetic beads by an electric field and opposingmagnetic field gradient. The electrophoretic force moves the beads inone direction, and the magnetic field gradient moves the beads in theopposite direction.

The present invention provides methods utilizing biological moleculesfor detecting and correcting errors that arise in the process ofconstructing long nucleic acid molecules. In one preferred embodiment ofthe invention, mismatch recognition can be used to control the errorsgenerated during oligonucleotide synthesis, gene assembly, and theconstruction of nucleic acids of different sizes. One of ordinary skillin the art will understand mismatch to mean a single error at thesequence position on one strand which gives rise to a base mismatch(non-complementary bases aligned opposite one another in theoligonucleotide), causing a distortion in the molecular structure of themolecule. In one aspect of the invention, mismatch recognition isachieved through the use of mismatch binding proteins (MMBP). The MMBPbinds to a mismatch in a DNA duplex; the MMBP-bound DNA complex is thenremoved using methods of protein purification well known to those havingordinary skill in the art. Another aspect of the invention allows forseparation of the MMBP-bound DNA complex using a difference in mobility,such as by size-exclusion column chromatography or gel electrophoresis.For methods and materials known in the art related to DNA mismatchdetection, see e.g., Biswas, I., Hsieh, P., Interaction of MutS Proteinwith the Major and Minor Grooves of a Heteroduplex DNA, JOURNAL OF BIO.CHEMISTRY, Vol. 272, No. 20, 13355-13364 (1997); Eisen, J. A., APhylogenomic Study of the MutS Family of Proteins, NUCLEIC ACIDSRESEARCH, Vol. 26, No. 18, 4291-4300 (1998); Beaulieu, M., Larson, G.P., Geller, L., Flanagan, S. D., Krontiris, T. G., PCR Candidate RegionMismatch Scanning: Adaption to Quantitative, High-Throughput Genotyping,NUCLEIC ACIDS RESEARCH, Vol. 29, No. 5, 1114-1124 (2001); Smith, J.,Modrich, P., Removal of Polymerase-Produced Mutant Sequences from PCRProducts, PROC. NATL. ACAD. SCI., 94, 6847-6850 (1997); Smith, J.,Modrich, P., Mutation Detection with MutH, MutL, and MutS MismatchRepair Proteins, PROC. NATL. ACAD. SCI., 93, 4374-4379 (1996); andBjornson, K. P., Modrich, P., Differential and Simultaneous AdenosineDi- and Triphosphate Binding by MutS, JOURNAL OF BIO. CHEMISTRY, Vol.278, No. 20, 18557-18562 (2003), all of which are hereby incorporated byreference. For patents relating to DNA mismatch repair systems, seee.g., U.S. Pat. Nos. 6,008,031, 5,922,539, 5,861,482, 5,858,754,5,702,894, 5,679,522, 5,556,750, 5,459,039, all hereby incorporated byreference.

In another aspect of the invention, a MMBP can be irreversibly complexedto an error containing DNA sequence by the action of a chemicalcrosslinking agent. The pool of DNA sequences is then amplified, butthose containing errors are blocked from amplification, and quicklybecome outnumbered by the increasing error-free sequences. In anotheraspect of the invention, DNA methylation may be used for strand-specificerror correction. Methylation and site-specific demethylation areemployed to produce DNA strands that are selectively hemi-methylated. Amethylase is used to uniformly methylate all potential target sites oneach strand, which are then dissociated and allowed to re-anneal withnew partner strands. A MMBP with demethylase complex is applied, whichbinds only to the mismatch. The demethylase portion of the complexremoves methyl groups only near the site of the mismatch. A subsequentcycle of dissociation and annealing allows the demethylatederror-containing strand to associate with a methylated error freestrand. The hemi-methylated DNA duplex now contains all the informationneeded to direct the repair of the error, employing the components of aDNA mismatch repair system.

In another aspect of the invention, local DNA on both strands at thesite of a mismatch may be removed and resynthesized to replace themismatch error. For example, a MMBP fusion to a non-specific nuclease(N) can bind to a mismatch site on DNA, forming a MMBP-nuclease DNAcomplex. The complex can then direct the action of the nuclease to themismatch site, and cleave both strands. Once the break is generated,homologous recombination can be employed to use other, error-freestrands as template to replace the excised DNA. Other mechanisms of DNAsynthesis well known in the art, such as strand invasion and branchmigration, may also be used to replace the excised DNA. Alternatively, apolymerase can be employed to allow broken strands to reassociate withnew full-length partner strands, synthesizing new DNA to replace theerror. In another aspect of the invention, the MMBP-nuclease-excised DNAcomplex can be physically separated from the remaining, error free DNAusing various techniques well known in the art. For methods andmaterials known in the art related to nucleases and fusion proteins, seee.g., Kim, Y., Chandrasegaran, S., Chimeric Restriction Endonucleases,PROC. NATL. ACAD. SCI., 91, 883-887 (1994); Kim, Y., Shi, Y., Berg, J.M., Chandrasegaran, S., Site-Specific Cleavage of DNA-RNA Hybrids byZinc Finger/FokI Cleavage Domain Fusions, GENE, 203, 43-49 (1997); Li,L., Wu, L. P., Chandrasegaran, S., Functional Domains in Fok IRestriction Endonuclease, PROC. NATL. ACAD. SCI., 89, 4275-4279 (1992);Kim, Y., Lowenhaupt, K., Schwartz, T., Rich, A., The Interaction BetweenZ-DNA and the Zab Domain of Double-Stranded RNA Adenosine DeaminaseCharacterized Using Fusion Nucleases, JOURNAL OF BIO. CHEMISTRY, Vol.274, No., 27, 19081-19086 (1999); Ruminy, P., Derambure, C.,Chandrasegaran, S., Salier, J., Long-Range Identification of HepatocyteNuclear Factor-3 (FoxA) High and Low-Affinity Binding Sites with aChimeric Nuclease, J. MOL. BIOL., 310, 523-535 (2001); Wah, D. A.,Bitinaite, J., Schildkraut, I., Aggarwal, A. K., Structure of FokI hasImplications for DNA Cleavage, PROC. NATL. ACAD. SCI., 95, 10564-10569(1998); and Wah, D. A., Hirsch, J. A., Dorner, L. F., Schildkraut, I.,Aggarwal, A. K., Structure of the multimodular endonuclease FokI boundto DNA, NATURE, 388, 97-100 (1997) all of which are hereby incorporatedby reference.

These and other aspects of the present invention will become evidentupon reference to the following detailed description. Additionally,various references are set forth herein. Each of these references ishereby incorporated by reference in its entirety as if each wasindividually noted for incorporation.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-F show an embodiment of the invention for generating long DNAsequences from oligonucleotides immobilized on a surface, such as anoligonucleotide microarray.

FIGS. 2A-G show an aspect of the invention for generating long DNAsequences from oligonucleotides synthesized on a surface, and thendetached from that surface into solution.

FIGS. 3A-D show an aspect of the invention for generating long DNAsequences starting from a set of many redundantly overlappedoligonucleotides, where the majority of the oligonucleotide sequence isused to generate the complementary overlap, thereby improving thepossibility of annealing.

FIG. 4 shows an aspect of the invention where the desired DNA sequenceencodes components needed for its own replication.

FIG. 5 shows an aspect of the invention for assembling long nucleotidesequences containing sites specifically designed to facilitate joiningof separate molecules. These sequences can be sites for specificendonuclease restriction and subsequent ligation, homologousrecombination, site-specific recombination, or transposition.

FIGS. 6A and 6B show an embodiment of the invention employing anall-biological synthetic strategy for the synthesis of bothsingle-stranded and double-stranded DNA using nucleotides with various3′-phosphate protecting groups, such as but not limited to, peptide,carbohydrate, diphosphate, or phosphate derivative 3′-phosphateprotecting groups.

FIG. 7 shows an embodiment of the invention employing an all-biologicalsynthetic strategy for the synthesis of double-stranded DNA using anoligonucleotide capping group.

FIGS. 8A-C show an embodiment of the invention employing anall-biological synthetic strategy for the synthesis of double-strandedDNA using oligonucleotide hairpin-loops as heat-removable protectinggroups.

FIGS. 9A and 9B show an embodiment of the invention employingforce-feedback, in this case optical tweezers and/or a magnetic trap, inorder to screen for and correct errors.

FIG. 10 shows an aspect of the invention employing force-feedback, inthis case electrophoresis, in order to screen for and correct errors.

FIGS. 11A and 11B show an embodiment of the invention employing parallelsingle-molecule systems using single and/or multiple arrays of lightsources and detectors to account for the possibility that an undetectedand/or uncorrected error may have occurred and to ensure that theprocess is successful.

FIGS. 12A and 12B show an aspect of the invention employing parallelsingle-molecule systems without arrays.

FIGS. 13A and 13B show a method for the microfabrication of quadrupolearrays.

FIGS. 14A and 14B show an embodiment of the invention for error checkingand error correction using nanopore devices for single-moleculesynthesis with feedback using fluorescent 5′ protecting groups.

FIGS. 15A-G illustrate the independent control of a cluster ofsuperparamagnetic beads by an electric field and opposing magnetic fieldgradient.

FIGS. 16A-C show an embodiment of the invention for removing errorsequences using mismatch binding proteins (MMBP). An error in a singlestrand of DNA causes a mismatch in a DNA duplex, which is selectivelybound by a MMBP and separated from error-free DNA by methods known inthe art such as by affinity capture or mobility differences.

FIG. 17 shows an aspect of the invention for removing and correctingerror sequences using chemical crosslinking agents complexed with MMBP.The pool of nucleotide sequences can then be amplified, and thosecontaining errors bound with the MMBP crosslinking agent complex will bequickly outnumbered by the error free nucleotide sequences.

FIG. 18 shows an aspect of the invention for strand-specific errorcorrection utilizing methylation and site-specific demethylation.

FIG. 19 shows an aspect of the invention for removing and correctingerror sequences using a MMBP fusion to a non-specific nuclease.

FIGS. 20A and 20B show an aspect of the invention for removing andcorrecting error sequences using a MMBP fusion to a non-specificnuclease. The MMBP binds to a mismatch in a DNA duplex; the MMBP-boundDNA complex is then removed using methods of protein purification.

FIGS. 21A and 21B show an aspect of the invention for removing andcorrecting error sequences using a MMBP fusion to a non-specificnuclease and both strand invasion and branch migration to synthesize theerror-free portions of the nucleotide sequence.

FIG. 22 shows an aspect of the invention for removing and correctingerror sequences using a MMBP fusion to a non-specific nuclease.

FIGS. 23A and B show an aspect of the invention for removing andcorrecting error sequences using a non-specific endonuclease to cut themolecule into shorter strands, binding error containing strands withMMBP, separating error containing MMBP complexed strands, and annealingand ligating cohesive ends.

FIG. 24 shows an aspect of the invention for removing and correctingerrors using recombination to generate templates for mismatchrecognition of errors.

FIG. 25 shows the results of the application of MutS to removal oferrors in DNA.

DETAILED DESCRIPTION OF THE INVENTION

Part I. Production of very long strands of nucleic acids.

Many protocols exist for assembling oligonucleotides into largermolecules of nucleic acid. These include ligase-based andpolymerase-based methods. Some of these methods combine all thenecessary oligonucleotides into a single pool for assembly (sometimesreferred to as “shotgun” assembly) while others assemble subsets of theoligonucleotides into larger sequences, and then combine these sequencesto yield the final full length product. Additionally, the fidelity ofthe initial library of short oligonucleotides often limits the fidelityof the full-length product. However, the production and manipulation ofoligonucleotides needed to produce molecules containing more than a fewthousand bases proves an arduous effort. This disclosure details methodsfor employing large numbers of oligonucleotides to efficiently generatemolecules of nucleic acid on this length scale, and much greater lengthscales as well. These methods can be applied to the generation of anextremely long molecule of nucleic acid, such as in the case of abacterial genome, or to the parallel production of many differentmolecules of nucleic acid of intermediate length, such as many variantsof a single gene. For methods and materials known in the art related toparallel production of biopolymers, see e.g., Lipshutz, R. J., Fodor, S.P. A., Gingeras, T. R., Lockhart, D. J., High Density SyntheticOligonucleotides Arrays, NATURE GENETICS SUPP., 21, 20-24 (1999);Pellois, J. P., Zhou, X., Srivannavit, O., Zhou, T., Gulari, E., Gao,X., Individually Addressable Parallel Peptide Synthesis on Microchips,NATURE BIOTECHOL., 20, 922-926 (2002); Gao, X., LeProust, E., Zhang, H.,Srivannavit, O., Gulari, E., Yu, P., Nishiguchi, C., Xiang, Q., Zhou,X., A Flexible Light-Directed DNA Chip Synthesis Gated by DetrotectionUsing Solution Photogenerated Acids, NUCLEIC ACIDS RES., Vol. 29, No.22, 4744-4750 (2001); and Singh-Gasson, S., Green, R. D., Yue, Y.,Nelson, C., Blattner, F., Sussman, M. R., Cerrina, F., MasklessFabrication of Light-Directed Oligonucleotide Microarrays Using aDigital Micromirror Array, NATURE BIOTECHOL., 17, 974-978 (1999) all ofwhich are hereby incorporated by reference.

According to the invention, the methods described herein can be appliedto 1) multiple kinds of nucleic acids (including ribonucleic acid,peptide-nucleic acid, locked-nucleic acid, and any combinationsthereof); and 2) other types of polymers, such as, but not limited to,RNA, PNA, LNA, etc. However, these examples are to be considered in allrespects illustrative rather than limiting on the invention describedherein. The examples given refer to, but are not limited to,deoxyribonucleic acid (DNA). According to the invention, the methodsdescribed herein may be performed in vivo or in vitro.

FIGS. 1A-F display a process of the invention for generating long DNAsequences from oligonucleotides immobilized on a surface, such as anoligonucleotide microarray. Such arrays are currently generated by avariety of synthetic approaches, including photolabile deprotection,photo-induced acid-labile deprotection, electrically-induced acid-labiledeprotection, and inkjet printing of reagents. The number of differentoligonucleotides that can be produced in microarray form is quite large.Some arrays may hold about 20,000 distinct locations, each with adifferent oligonucleotide sequence. The highest density arrays cancontain about 400,000 distinct locations per square centimeter. For anarray of 50-mer oligonucleotides, this would correspond to 20 millionbases, roughly four times the genome size of many common bacteria.

FIG. 1A. The desired double-stranded DNA sequence to be produced,labeled in sections. Arrowheads indicate the 3′ end of each DNA strand.Complementary sections of the top and bottom strand are indicated as A,A′, and so forth.

FIG. 1B. A portion of an oligonucleotide microarray containing all theoligonucleotide sequences necessary for generating the sequence of FIG.1A. Each region of the microarray (1, 2, 3, . . . ) containsoligonucleotides of a single, distinct sequence, with only a singlestrand from each shown for clarity. The oligonucleotides are covalentlyattached to the surface indicated, and are immersed in a solutionsuitable for performing enzymatic reactions such as PCR.

FIG. 1C. An oligonucleotide primer equivalent to the sequence of DNAsection “A” is added to the solution. The sequence of thisoligonucleotide is complementary to that of immobilized oligonucleotide1 (which contains sequences A′ and B′) and will selectively hybridize tothe A′ region of that oligonucleotide, producing a region ofdouble-stranded DNA.

FIG. 1D. The action of a DNA polymerase, such as those used for PCR(e.g. Taq, Pwo, Pfu) is used to extend the primer, adding sequence B.

FIG. 1E. Sequence AB is dissociated from oligonucleotide 1 (A′B′). Thiscan be accomplished using conventional PCR thermocyclers adapted forflat supports (typically used with glass slides for in situ PCR) Thefree AB sequence is moved through the solution (by the action ofdiffusion, bulk liquid flow, electrophoresis, or using attached magneticparticles) to the site of oligonucleotide 2 (containing sequence B′C′).

FIG. 1F. As in FIG. 1D, a DNA polymerase extends sequence AB to yieldsequence ABC. Repetition of the steps of dissociation, annealing, andextension are used to produce the DNA sequence of desired length.

One advantage of the method shown in FIGS. 1A-F is the ability to trackthe progress and growth of the product by fluorescence. The freeoligonucleotide corresponding to the 5′ end of the sequence can includea fluorescent group at the 5′ terminus. As the growing chain anneals todifferent spots on the microarray, regions of high concentration of thefluorescent group (where the free oligonucleotide is bound) are detectedby fluorescence microscopy. Thus, the progress of the growing chain canbe monitored. For example, fluorescence at oligonucleotide spot 3indicates that the growing free DNA chain must contain at least sequenceABC in order to anneal. This monitoring is especially useful in the caseof potential mis-annealing between sequences which are similar, but notthe intended (perfect) match. In this case, the presence of afluorescent spot at an unexpected location shows which sequence the freeoligonucleotide has annealed to.

Another aspect of this invention is the stepwise repositioning of thegrowing DNA chain as a means to control the movement of some additionalcomponent. Referring to FIGS. 1A-F, for the first cycle of annealing,the attached component will only be present at spot 1. Following strandextension by polymerase, the sequence attached to the component now hasthe sequence AB. In the second cycle of annealing, this complex willadvance no further than spot 2, and so forth. The attached growing chainwill still also have affinity for spot 1, and will be partiallylocalized there as well. However, the component and attached DNA chaincan be “chased” through the spot locations by adding an excess of freeoligonucleotide sequence A in a later cycles. For example, adding excessA in cycle 2 means that free oligonucleotide A will compete with theAB-attached component to anneal to spot 1 (in essence, flushing theAB-attached component away from this site), but only the AB-attachedcomponent will have affinity for site 2 (via the interaction betweenB-B′ sequences).

In a preferred embodiment of the invention, the oligonucleotides to beused will be synthesized in a parallel format, such as in anoligonucleotide microarray. The oligonucleotides will be detached fromtheir support and manipulated, for example, by a microfluidic device forthe purpose of assembly into larger molecules of nucleic acid. Theoligonucleotides can be detached selectively or in groups.Oligonucleotides produced in this device could also be used for otherprocesses affecting the amount and quality of the final product:examples include affinity purification, amplification, sequencing, andmutagenesis. Means to manipulate oligonucleotides and other nucleic acidmolecules in this device are well known in the art, and include but arenot limited to, passive diffusion, liquid flow, electrophoresis,attachment to a movable solid support such as a magnetic bead, andaffinity for nucleic acid or other molecules.

FIGS. 2A-G show a process of the invention for generating long DNAsequences from oligonucleotides synthesized on a surface, and thendetached from that surface.

FIG. 2A. The desired DNA sequence to be produced, labeled in sections.As in FIG. 1, arrowheads indicate the 3′ end of each DNA strand.Complementary sections of the top and bottom strand are indicated as A,A′, and so forth.

FIG. 2B. A portion of an oligonucleotide microarray containing all theDNA sequences necessary for producing the full length sequence of FIG.2A. Each region (1, 2, 3, . . . ) contains oligonucleotides of a single,distinct sequence, with only a single strand of each shown for clarity.The oligonucleotides are covalently attached to the surface via acovalent linker that can be cleaved (using chemistry similar to that ofconventional oligonucleotide synthesis, in which the final product iscleaved from a solid support on a column, or by other methods such asphotolabile chemistry).

FIG. 2C. The oligonucleotides are cleaved from the surface, releasingthem into solution.

Production of larger DNA sequences can proceed using either thepolymerase chain reaction (PCR, using a thermostable DNA polymerase) ora ligase reaction (including LCR, ligase chain reaction, using athermostable DNA ligase). A variety of related gene synthesis approachesare also possible at this step.

FIG. 2D. The complementary regions of the oligonucleotides associate tocreate regions of double-stranded DNA. (Only some of these combinationsare shown for clarity.) This process can occur using theoligonucleotides directly as released from the original surface, orafter a concentration step using electrophoresis, osmotic filtration, orsimple evaporation. A microfluidic device can be employed to aid in themanipulation, combination, and concentration of oligonucletides. Such ause is particularly desirable in the case of producing a set of distinctand separate DNA sequences from a single microrray, such as producingmany variants of the same gene. Such a use is also particularlydesirable for the manipulation of DNA sequences for DNA computing. Formethods and materials known in the art related to microfluidic devices,see e.g., Lagally, E. T., Medintz, I., Mathies, R. A., Single-MoleculeDNA Amplification and Analysis in an Integrated Mircrofluidic Device,ANAL. CHEM., 73, 565-570 (2001), which is hereby incorporated byreference.

FIG. 2E. A DNA polymerase extends the 3′ ends of the oligonucleotides,producing larger DNA duplexes.

FIG. 2F. DNA duplexes are dissociated and allowed to reanneal. One ofthe resulting new duplexes is shown.

FIG. 2G. DNA polymerase again extends the 3′ ends of the annealedoligonucleotides, producing still larger DNA duplexes. The process ofdissociation, annealing, and extension is then repeated over multiplecycles, allowing increasingly longer DNA sequences to be assembled,producing the desired target sequence.

In conventional gene assembly, oligonucleotides are synthesized torepresent the complete sequence, with overlaps designed between pairsfor annealing prior to extension by a DNA polymerase or ligation by aDNA ligase. As the size of the target sequence grows, so does the numberof oligonucleotides needed to assemble it. As the number ofoligonucleotides grows, the potential for oligonucleotides to partnerwith incorrect strands also increases. This problem can be addressedpartially by employing higher temperatures for the annealing conditions,minimizing the chance of mis-partnering. This approach generallyrequires longer overlaps, and thus longer oligonucleotides. For anoligonucleotide of a given length, up to half that length is used toform each overlap. However, using a synthesis method of the inventionwith the scale of synthesis possible on a single microarray (tens ofthousands or more of oligonucleotides of distinct sequences), it becomespractical to use an even higher proportion of the oligonucleotides toform each overlap. Thus the maximal specificity of annealing is achievedin this aspect of the invention by including many oligonucleotides ofclosely spaced sequence. At the same time, the length of theoligonucleotide may be kept to a minimum, which reduces some types oferrors inherent in oligonucleotide synthesis. For methods and materialsknown in the art related to the synthesis of nucleic acids usingmicroarrays, see e.g., McGall, G. H., Barone, A. D., Diggelmann, M.,Fodor, S. P. A., Gentalon, E., Ngo, N., The Efficiency of Light-DirectedSynthesis of DNA Arrays on Glass Substratesi, J. AM. CHEM. SOC., Vol.119, No. 22, 5081-5090 (1997), which is hereby incorporated byreference.

FIGS. 3A-D show the synthesis of a large DNA molecule starting from aset of many redundantly overlapped oligonucleotides. As in FIGS. 2A-G,assembly relies on annealing complementary pairs of oligonucleotides andextending them to produce longer segments of DNA, until the full-lengthsequence is produced. However, in this case, the majority of theoligonucleotide sequence is used to generate the complementary overlap,improving the maximum possible specificity of annealing. Though thefirst polymerase extensions only produce slightly larger pieces of DNA,later growth steps are still exponential. Also, sometimes a particularoligonucleotide synthesis may fail, or be especially inefficient. Formethods and materials known in the art related to nucleotide synthesisinvolving overlapped oligonucleotides see, e.g., European PatentApplication EP 1314783A1 titled Nukleinsaure-Linker und deren Verwendungin der Gensynthese assigned to Sloning BioTechnology GmbH, which ishereby incorporated by reference.

This approach provides “insurance” against the failure of the synthesisof any one distinct oligonucleotide sequence. For example, in FIGS.2A-G, a failure to produce oligonucleotide sequence CD would result inan inability to produce the longer CDE and ABCDE strands. In contrast,removal of any one oligonucleotide shown in FIG. 3B does not preventassembly of the full-length molecule. Thus, the many possible overlapsensure that even if one oligonucleotide (such as oligonucleotide 2) wereremoved, the full-length assembly will still be achievable, because thefull-length sequence is encoded redundantly in multipleoligonucleotides.

FIG. 3A. The desired target sequence, divided into segments labeled A,B, C, and so forth.

FIG. 3B. Both top and bottom strands of the target sequence arerepresented redundantly by multiple oligonucleotides (1, 2, 3, etc forthe top strand, and 1′, 2′, 3′ etc for the bottom).

FIG. 3C. Under the most stringent annealing conditions (such as hightemperature), only the oligonucleotides with a high degree ofcomplementarity will anneal (such as 1 and 2′), giving rise to DNAduplexes which can be extended from their 3′ ends.

FIG. 3D. If the synthesis of a particular oligonucleotide fails (such as2′) the overall gene synthesis need not fail, since under only slightlyless stringent conditions the next oligonucleotide in the set alsocontains the necessary sequence to anneal (such as 1 and 3′). Thispossibility can be seamlessly introduced into the annealing protocol bygradually reducing the temperature used. Thus the most specificinteractions dominate (longest overlaps, highest melting temperatures),but interactions that are only slightly less specific (like the 1-3′annealing) will also be allowed. In the case of PCR, this progressivelowering of annealing temperature, known to those having ordinary skillin the art as “touchdown PCR”, is distinct in this invention in itsapplication to redundantly overlapped sets of oligonucleotides.

FIG. 4 illustrates the special case when the desired DNA sequenceencodes components needed for its own replication. If the goal of theDNA production is not to generate a particular exact DNA sequence, butrather to produce a function (or a set of functions), then that functioncan be used to screen the pool of DNA molecules for the successfulproducts. For example, the desired product can be a phage, such as abacteriophage, that is capable of replicating in its host. The methodspreviously discussed could then be used to generate a long DNA moleculecontaining the phage genome. This DNA molecule could be used to producephage particles using in vitro transcription and/or in vitrotranslation. Alternatively, the DNA could be transfected directly intothe host, or treated with a packaging extract to form virus/phageparticles. Regardless, only DNA molecules containing the propercomponents for the phage life cycle will survive this selection process,and produce viable phage. But the sequence selected for can be thegenome of an entire organism, such as a bacterium. The functional screenwould then be whether the organism is capable of producing a functionalmetabolism capable of growth, leading to DNA replication and eventuallycell division.

FIG. 4. The desired sequence (such as for a phage) has been produced bythe aforementioned methods, or by conventional gene synthesistechniques. Regardless of the method, many of the sequences may containerrors. In vitro transcription is employed to produce an RNA transcriptof the phage DNA. Alternatively, the DNA can be transfected into a hostwhich performs the transcription. In vitro translation of the RNA hasbeen performed to produce proteins needed for the phage life cycle, suchas packaging of the phage genome (DNA or RNA, depending on theparticular phage). Alternatively, translation can also occur within asuitable host. The phage genome (DNA or RNA) is packaged by the phageproteins, producing phage particles. The phage particles which containfunctional packaging proteins can infect host cells, and thosecontaining a viable copy of the phage genome can go on to produceinfectious particles within the host.

An aspect of the invention is that such DNA products are alsointrinsically more error-tolerant. The DNA produced may containdeviations from the user-specified sequence. But if these deviationsresult in silent or tolerable mutations to the coding regions, orinconsequential changes outside the coding regions, then they areimmaterial to the success of the final product. On the other hand,errors which impair the ability of the phage to replicate do not resultin viable phage particles, and are therefore not observed in the finalproduct.

When assembling especially long nucleic acid sequences, processes suchas PCR will eventually become ineffective. For example, a typical lengthof time recommended for polymerase-based extension in a cycle of PCR is1 minute per kb of DNA synthesized. For a 1-10 kb sequence this is apractical parameter, but for 100 kb it becomes cumbersome, and 1000 kbof linear sequence would require over 16 hours for a single cycle. Knownpolymerases are not sufficiently processive to accomplish this. And,since many PCR cycles are also typically employed, the total timeinvolved to assemble and/or amplify DNA sequences on this scale becomesa great challenge.

FIG. 5 shows a method for assembling long DNA sequences. Each sequencecontains one or more regions containing sites specifically designed tofacilitate joining of the separate molecules. These sequences can besites for specific endonuclease restriction and subsequent ligation,homologous recombination, site-specific recombination (such as used bysome viral integrases), or transposition. The joining sites need not beat the ends of linear DNA. In fact, the starting and final molecules canbe linear DNA, circular DNA, or some combination. FIG. 5 illustrates thehomologous recombination of linear DNA duplexes. These processes can beperformed in vitro, though there will be advantages to performing themin living organisms as well, such as the use of host factors tofacilitate the process of joining, as well as the use of hostreplication machinery to ensure the most efficient and accurateamplification of the exogenous DNA. Such joining mechanisms are found innature and are well known to those having ordinary skill in the art forcombining DNA molecules of various sizes. For example, an organism suchas Deinococcus radiodurans is able to reassemble its entire genome evenafter it has been sheared into many separate pieces. A novel aspect ofthis invention is the application of these procedures to generate largeDNA molecules whose entire sequences are completely determined by theuser de novo (as opposed to simply being derived from an organism, suchas by conventional cloning).

FIG. 5. Three long DNA sequences, with end regions specifically designedfor homologous recombination. The A and A′ ends of the top two DNAduplexes undergo homologous recombination, joining these into a longerduplex. The same type of joining occurs between the bottom two duplexes,using a different set of homologous sequences, B and B′.

This disclosure also details methods for an ‘all-biological linearsynthesis’ of nucleic acids. This synthetic strategy employs the use ofbiological molecules as protecting groups, and all nucleotide additionand deprotection steps are performed using biological enzymes. Such asynthetic technique will ultimately yield nucleotides that are longerand have higher fidelity (i.e. have less errors) than those synthesizedby standard techniques. The synthesis is performed in biologicalconditions (aqueous environment at neutral pH), thereby eliminating thedamage to the nucleotides during the process. Since the synthesisproceeds in the 5′-3′ direction, biological enzymes can be used forsubtractive error-correction at the 3′ terminus—an option not availablein standard solid-phase synthetic schemes. For methods and materialsknown in the art related to protecting groups, see e.g., Muller, C.,Even, P., Viriot, M., Carre, M., Protection and Labelling of Thymidineby a Fluorescent Photolabile Group, HELVETICA CHIMICA ACTA, 84,3735-3741 (2001) and Fedoryak, O. D., Dore, T. M., BrominatedHydroxyquinoline as a Photolabile Protecting Group with Sensitivity toMultiphoton Excitation, ORGANIC LETTERS, Vol. 4, No. 20, 3419-3244(2002) all of which are hereby incorporated by reference.

An all-biological synthetic strategy is particularly attractive whencoupled with the single-molecule feedback and error-correcting schemesin this disclosure. These schemes typically utilize electrophoreticforce measurements, based on the intrinsic negative-charge of the DNAphosphate backbone, as the feedback mechanism during nucleotide additionsteps. Oligonucleotides generated by an all-biological synthetic schemeare always negatively charged at each step in the cycle. Thus, thisprocess provides a negatively charged backbone compared to the standard(phosphoramidite) approach, where the backbone is neutral until theoligonucleotide has reached its full-desired length.

FIG. 6A. Synthesis of single-stranded DNA with a peptide or carbohydrate3′-phosphate protecting group. After an addition to the nascent DNAstrand (SEQ ID NO.: 1) by a capped nucleotide or oligonucleotide, aprotease cleaves the bond between the capping group and the mostrecently added nucleotide, forming an oligonucleotide (SEQ ID NO.: 2)comprising one more nucleotide base than the nascent DNA strand. Themonomer addition can be done with traditional chemical synthesis orenzymatically (by using a terminal transferase or nucleotide ligase).DNA polymerase or nucleotide ligase can be used to add a 3′ cappednucleotide or oligonucleotide to the 3′ end of the nascent strand. DNAligase can also be used to add a 5′ capped nucleotide or oligonucleotideto the 5′ end of the nascent strand. A sample method comprises the useof a tyrosine residue bound to the 3′ hydroxyl of the newly addedmonomer as a capping group. Tyrosyl-DNA phosphodiesterase is used toeliminate the capping group and continue addition of new monomers.Aminoacyl hydrolase, Proteinase K or an evolved enzyme can be used toeliminate other peptide capping groups.

FIG. 6B. Synthesis of single-stranded DNA with diphosphate or phosphatederivative as a 3′-phosphate protecting group. After an addition to thenascent DNA strand (SEQ ID NO.: 3) by a capped nucleotide oroligonucleotide, forming an oligonucleotide (SEQ ID NO.: 4) comprisingone more nucleotide base than the nascent DNA strand, a phosphatasecleaves the bond between the capping group and the most recently addednucleotide. The monomer addition can be done with traditional chemicalsynthesis or enzymatically (by using a terminal transferase ornucleotide ligase). DNA polymerase or nucleotide ligase can be used toadd a 3′ capped nucleotide or oligonucleotide to the 3′ end of thenascent strand. DNA ligase can also be used to add a 5′ cappednucleotide or oligonucleotide to the 5′ end of the nascent strand. Thecapping group is a single phosphate at the 3′ or 5′ end of the monomer(depending on the chemistry), a 2′3′ cyclic phosphate, or multiplebeaded phosphate groups, or other phosphate derivatives. Adeoxynucleotide 3′ phosphatase, cleaves phosphates from the 3′ end ofthe nascent strand after a nucleotide or oligonucleotide addition hasoccurred, leaving a free 3′ hydroxyl. In the cyclic phosphate case, 2′3′cyclic nucleotide 2′ phosphodiesterase and deoxynucleotide 3′phosphatase together cleave the cyclic phosphate and free a 3′ hydroxyl.

FIG. 7. Synthesis of a double-stranded DNA with an oligonucleotidecapping group. The capping group is comprised of a nucleotide or shortoligonucleotide that can be cleaved by a restriction enzyme from thenascent double stranded DNA (SEQ ID NO.: 1; SEQ ID NO.:5). Theoligonucleotide cap may or may not form a DNA secondary structure suchas a hairpin loop. After the addition of a capped nucleotide oroligonucleotide, which forms a double stranded oligonucleotide (SEQ IDNO.: 6, SEQ ID NO.: 7) comprising additional nucleotide bases ascompared to the nascent double-stranded DNA, a restriction enzyme whichrecognizes the capping nucleotide sequence will cleave the fragment 3′to the newly added nucleotide, resulting in a double strandedoligonucleotide (SEQ ID NO.: 2, SEQ ID NO.: 8) comprising an additionalnucleotide base pair as compared to the nascent double-stranded DNA. AdsDNA oligonucletide with the desired nucleotide or oligonucleotide tobe added would also contain a restriction site 3′ to the leading strand,whose 3′ end of the leading strand would possess a 2′3′ dideoxynucleotide (or other capping group such that prevents multiple monomeraddition) and the lagging strand a 5′ deoxy ribose (or other cappinggroup that prevents multiple monomer addition). For this particularscheme a Type III or other restriction endonuclease would be used to cutoutside of the recognition site, thus leaving only the nascent strandwith the newly added nucleotide or oligonucleotide. Thereby, thesequence of the monomer is X—R where X is a specific nucleotide oroligonucleotide sequence that will be added to the nascent strand bynucleotide ligase and R is the restriction enzyme recognition site whichwill be cleaved after ligation of the new monomer. The desirednucleotide (X) will remain on the nascent strand. This procedure isrepeated to create a specific oligonucleotide sequence. Differentrestriction enzymes and corresponding capping nucleotides or sequenceredesign may be required for the creation of desired oligonucleotides inorder to prevent sequence recognition in the nascent strand. DNA ligaseor topoisomerase may be covalently bound to the end or beginning of themonomer to facilitate monomer addition.

FIGS. 8A-C. Synthesis of double-stranded DNA using oligonucleotidehairpin-loops as heat-removable protecting groups. Oligonucleotides withsecondary conformational structures, such as DNA hairpin-loops (alsotermed stem-loops, and molecular beacons), can also be used asprotecting groups. A similar approach has been reported wherehairpin-loops are enzymatically removed by restriction enzymes, aprocess termed “synthetic cloning” or “splinking.” The methods describedin FIGS. 8A-C differ from previously reported methods in the generalstructure of the hairpin-loops, and because the removal method is gentleheating. Furthermore, gentle heating is potentially an improved methodof deprotection over enzymatic removal because 1) heat distributes morequickly and uniformly than enzymes because the enzymatic removal rate isdiffusion-limited, and 2) gentle heating is a lower-cost resource thanrestriction enzymes.

FIG. 8A. In this scheme for double-stranded DNA synthesis, the monomerunit that is added to the growing nascent strand is a complex comprisedof DNA hairpin-loop (SEQ ID NO.: 9) and an annealed shortoligonucleotide insert segment. Additional monomers are first producedby annealing a hairpin-loop and a partially complementary shortoligonucleotide insert segment. At one end, the insert segment sequencehas at least one base which is complementary to the last base added tothe nascent strand, and at the other end of the insert sequence there isat least 1 base which is complementary to its respective hairpin cappinggroup. Both the 5′ and 3′ ends of the hairpin structure lack reactivehydroxyl groups so are unable to ligate to the insert strand or nascentstrand. After hairpins and inserts are annealed, they are purified suchthat only single hairpin-insert monomers (SEQ ID NO.: 10) are present.The hairpin-insert monomers are added to the nascent double strand (SEQID NO.: 11, SEQ ID NO.: 12) and DNA ligase is used to ligate the insertsegment to the nascent strand, forming a double-stranded oligonucleotidewith a hairpin (SEQ ID NO.: 13) that comprises additional bases ascompared to the nascent double-stranded DNA. The capping group isremoved by varying the pH or temperature of the solution and furthermonomers added to create a specific double stranded oligonucleotidesequence (SEQ ID NO: 14, SEQ ID NO.: 12).

FIG. 8B. Synthesis of single-stranded DNA by PCR using a DNAhairpin-loop as both the PCR primer and the protecting group. Thehairpin-loop monomer contains three regions: 1) a partiallycomplementary oligonucleotide sequence at the 5′ end that serves as thePCR primer (X), 2) an oligonucleotide sequence that serves as thetemplate for the polymerization (Y), and 3) terminal hairpin-loop thatserves as the protecting group (Z). First, the partially complementaryregion of the hairpin-loop (X) anneals to the nascent strand. Second,polymerase proceeds to copy the template region of the hairpin-loop (Y).The hairpin-loop monomer is capped at both the 5′ and 3′ ends, andtherefore, is incapable of being incorporated into the growing nascentstrand during the polymerization step. The polymerization reactionterminates at the 3′-end of the hairpin-loop monomer because it isprotected. The hairpin-loop is removed by gentle heating. Because the5′-end of the hairpin-loop is capped, the addition to the growingoligonucleotide is single-stranded.

FIG. 8C. Synthesis of double-stranded DNA by PCR using a DNAhairpin-loop as both the PCR primer and the protecting group. Thesynthetic approached presented in FIG. 8B can also be used to synthesizedouble-stranded DNA. Prior to removing the hairpin-loop by heating inthe scheme described in FIG. 8B, a short oligonucleotide (W) isintroduced that is complementary to the growing single-strand (bottomstrand in the figure). The oligonucleotide (W) is added to the topstrand of the growing chain by polymerase or ligase. After this additionstep, the hairpin-loop is removed by gentle heating. When synthesizingvery long DNA, the double-stranded synthesis approach shown in FIG. 8Cis preferred over the single-strand approach shown in FIG. 8B because ofthe increased probability that the hairpin-loop anneals to the terminusof the growing strand.

Part II. DNA error control.

In the process of constructing long molecules of nucleic acid, one needsto confront the potential errors that are expected to arise in thosemolecules. As the molecule length grows, conventional methods oferror-reduction, such as denaturing high performance liquidchromatography (DHPLC), become prohibitively cumbersome, time-consuming,and costly. Feedback and quality control in standard batch synthesisprocedures are often employed, such as spectroscopic and potentiometricmonitoring of the removal of 5′-protecting groups, and iterative DHPLCpurification. However, spectroscopic and potentiometric monitoring donot provide information on individual oligonucleotides strands beingsynthesized, and quality control by purification does not provide 100%sequence fidelity. A novel aspect of this invention presents a methodfor dramatically reducing errors in synthesized molecules of nucleicacid.

Biological organisms have means to detect errors in their own DNAsequences, as well as repair them. One component of such a system is amismatch binding protein which can detect short regions of DNAcontaining a mismatch, a region where the two DNA strands are notperfectly complementary to each other. Mismatches can be the result of apoint mutation, deletion, insertion, or chemical modification. For thepurpose of this invention, a mismatch includes base pairs of opposingstrands with sequence A-A, C-C, T-T, G-G, A-C, A-G, T-C, T-G, or thereverse of these pairs (which are equivalent, i.e. A-G is equivalent toG-A), a deletion, insertion, or other modification to one or more of thebases. The mismatch binding proteins (MMBPs) have previously been usedcommercially for the detection of mutations and genetic differenceswithin a population (SNP genotyping), but prior to this disclosure, havenot been used for the purpose of error control in designed sequences.Many representative proteins exist capable of mediating activities ofmismatch recognition, endonuclease activity, and recombination activity.For example, recombination activity may be accomplished using somesubset of the phage Lambda proteins Exo, Gam, Beta, or their functionalhomologs. For example, mismatch recognition may be perfomed by MutS orone of its functional homologs. For methods and materials know in theart relating to mismatch recognition, endonuclease activity, andrecombination activity, see e.g., Yang, B., Wen, X., Kodali, S.,Oleykowski, C. A., Miller, C. G., Kulinski, J., Besack, D., Yeung, J.A., Kowalski, D., Yeung, A. T., Purification, Cloning, andCharacterization of the CEL I Nuclease, BIOCHEMISTRY, 39, 3533-3541(1999); Youil, R., Kemper, B., Cotton, R. G. H., Detection of 81 of 81Known Mouse β-Globin Promoter Mutations with T4 Endonuclease VII—The EMCMethod, GENOMICS, 32, 431-435 (1995); Jackson, B. A., Barton, J. K.,Recognition of DNA Base Mismatches by a Rhodium Intercalator, J. AM.CHEM. SOC., 119, 12986-87 (1997); Nakatani, K., Sando, S., Saito, I.,

According to the invention, mismatch recognition can be used to controlthe errors generated during oligonucleotide synthesis, gene assembly,and the construction of nucleic acids of different sizes. (Thoughbiological systems use this function when synthesizing DNA, it requiresthe presence of a template strand. For de novo synthesis, employed forthis invention, one is starting by definition without a template.)Mismatch recognition can be accomplished by the action of a protein(such as bacterial MutS proteins, eukaryotic MSH proteins, T4endonuclease VII, T7 endonuclease I, and celery CelI) a small molecule(for example dimeric 2-amino-1,8-naphthyridine), or a process (such astemperature gradient gel electrophoresis or denaturing HPLC). In apreferred embodiment of the invention, recognition is accomplishedemploying a mismatch recognition protein such as MutS or its functionalhomologs.

When attempting to produce a desired DNA molecule, a mixture typicallyresults containing some correct copies of the sequence, and somecontaining one or more errors. But if the synthetic oligonucleotides areannealed to their complementary strands of DNA (also synthesized), thena single error at that sequence position on one strand will give rise toa base mismatch, causing a distortion in the DNA duplex. Thesedistortions can be recognized by a mismatch binding protein. (Oneexample of such a protein is MutS from the bacterium Escherichia coli.)Once an error is recognized, a variety of possibilities exist for how toprevent the presence of that error in the final desired DNA sequence.

When using pairs of complementary DNA strands for error recognition,each strand in the pair may contain errors at some frequency, but whenthe strands are annealed together, the chance of errors occurring at acorrelated location on both strands is very small, with an even smallerchance that such a correlation will produce a correctly matchedWatson-Crick base pair (e.g. A-T, G-C). For example, in a pool of 50-meroligonucleotides, with a per-base error rate of 1%, roughly 60% of thepool (0.99⁵⁰) will have the correct sequence, and the remaining fortypercent will have one or more errors (primarily one error peroligonucleotide) in random positions. The same would be true for a poolcomposed of the complementary 50-mer. After annealing the two pools,approximately 36% (0.6²) of the DNA duplexes will have correct sequenceon both strands, 48% (2×0.4×0.6) will have an error on one strand, and16% (0.4²) will have errors in both strands. Of this latter category,the chance of the errors being in the same location is only 2% ( 1/50)and the chance of these errors forming a Watson-Crick base pair is evenless (⅓× 1/50). These correlated mismatches, which would go undetected,then comprise 0.11% of the total pool of DNA duplexes (16×⅓× 1/50).Removal of all detectable mismatch-containing sequences would thusenrich the pool for error-free sequences (i.e. reduce the proportion oferror-containing sequences) by a factor of roughly 200 ( 0.6/0.4originally for the single strands vs. 0.36/0.0011 after mismatchdetection and removal). Furthermore, the remaining oligonucleotides canthen be dissociated and re-annealed, allowing the error-containingstrands to partner with different complementary strands in the pool,producing different mismatch duplexes. These can also be detected andremoved as above, allowing for further enrichment for the error-freeduplexes. Multiple cycles of this process can in principle reduce errorsto undetectable levels. Since each cycle of error control may alsoremove some of the error-free sequences (while still proportionatelyenriching the pool for error-free sequences), alternating cycles oferror control and DNA amplification can be employed to maintain a largepool of molecules.

According to the invention, if the DNA duplexes in question have beenamplified by a technique such as the polymerase chain reaction (PCR) thesynthesis of new (perfectly) complementary strands would mean that theseerrors are not immediately detectable as DNA mismatches. However,melting these duplexes and allowing the strands to re-associate with new(and random) complementary partners would generate duplexes in whichmost errors would be apparent as mismatches, as described above.

Many of the methods described below can be used together, applyingerror-reducing steps at multiple points along the way to producing along nucleic acid molecule. Error reduction can be applied to the firstoligonucleotide duplexes generated, then, for example, to intermediateoligonucleotides of about 500-mers to about 1000-mers, and then even tolarger full length nucleic acid sequences of about 10,000-mers or more.

This invention provides methods for dramatically reducing errors inlarge-scale gene synthesis. It is possible to generate the nucleic acidof interest by direct linear synthesis, but on a length scale previouslymade impossible by the error rates associated with chemical synthesis ofoligonucleotides. For the purpose of this invention, direct observationof products at the single-molecule level during the synthesis processprovides a means to monitor and even correct errors that occur duringsynthesis. Since DNA can be amplified by PCR, large amounts ofoligonucleotides can be copied from perfect oligonucleotide with thefidelity of polymerase activity (one error in 10³-10⁸).

There are several observation methods for single-molecule techniques,such as single-molecule fluorescence spectroscopy, nanopore analysis,and force microscopy using atomic force microscopes, optical tweezers,and magnetic tweezers. Direct observation of single-molecules enablesfeedback during the synthesis of an individual oligonucleotide.Therefore, the time per addition (nucleotide or short oligonucleotide)is minimized, whereas typical addition times are in excess in order tomaximize the yield per step. Furthermore, feedback at thesingle-molecule level also enables error-correction, thereby greatlyincreasing the fidelity of the oligonucleotide.

The methods described herein can employ various optical tweezers andmagnetic tweezers, electrophoretic techniques, and microscopytechniques. Designs of optical and magnetic tweezers include, but arenot limited to: 1) single-beam optical tweezers that trap one particle,2) single-beam optical tweezers that trap multiple particles, 3)parallel multiple-beam optical tweezers, 4) optical tweezers withsingle-molecule fluorescence detection capability, 5) single-pole,double-pole, quadrupole, sextapole, octapole magnetic tweezers usingelectromagnetic coils, 6) single-pole and double-pole tweezers usingpermanent magnets, 7) parallel multiple-pole magnetic tweezers, and 8)magneto-optical tweezers. Single-molecule electrophoretic techniquesinclude, but are not limited to: 1) electrophoresis in a static electricfield, 2) electrophoresis in a variable electric field, and 3) capillarygel electrophoresis. For methods and materials known in the art relatedto electrophoresis, see e.g., Wu, X., Kasashima, T., An Improvement ofthe On-Line Electrophoretic Concentration Method for CapillaryElectrophoresis of Proteins and Experimental Factors Affecting theConcentration Effect, ANALYTICAL SCIENCES, 16, 329-331 (2000), which ishereby incorporated by reference. Single-molecule microscopy techniquesinclude, but are not limited to: 1) fluorescence with single-photonexcitation, 2) fluorescence with multi-photon excitation, 3)differential phase contrast microscopy, and 4) differential interferencecontrast microscopy. These examples are to be considered in all respectsillustrative rather than limiting on the invention described herein. Formethods and materials known in the art related to various magnetic,optical, magneto-optical, electromagnetic, dipole, and quadrupole traps,see e.g., Goose, C., Croquette, Magnetic Tweezers: Micromanipulation andForce Measurement at the Molecular Level, BIOPHYS. J., 82, 3314-29(2002); Sacconi, L., Romano, G., Ballerini, R., Capitanio, M., De Pas,M., Giuntini, M., Three-Dimensional Magneto-Optic Trap for Micro-ObjectManipulation, OPTICS LETTERS, Vol. 26, No. 17, 1359 (2001); Wirtz, D.,Direct Measurement of the Transport Properties of a Single DNA Molecule,PHYSICAL REVIEW LETTERS, Vol. 75, No. 12, 2436 (1995); Tanase, M.,Hultgren, A., Searson, P. C., Meyer, G. J., Reich, D. H., MagneticTrapping of Multicomponent Nanowires, (2001); Amblard, F., Yurke, B.,Pargellis, A., Leibler, S., A Magnetic Manipulator for Studying LocalRheology and Micromechanical Properties of Biological Systems, REV. SCI.INSTRUM., Vol. 67, No. 3, 819 (1996); Lee, C. S., Lee, H., Westervelt,R. M., Microelectromagnets for the Control of Magnetic Nanoparticles,APPL. PHYS. LETT., Vol. 79, No. 20, 3308 (2001); Garbow, N., Evers, M.,Palberg, T., Optical Tweezing Electrophoresis of Isolated, HighlyCharged Colloidal Spheres, COLLOIDS AND SURFACES A: PHYSIOCHEM. ENG.ASPECTS, 195, 227-241 (2001); Lang, M. J., Asbury, C. L., Shaevitz, J.W., Block, S. M., An Automated Two-Dimensional Optical Force Clamp forSingle Molecule Studies, BIOPHYS. J., 83, 491-501 (2002); Galneder, R.,Kahl, V., Arbuzova, A., Rebecchi, M., Radler, J. O., McLaughlin, S.,Microelectrophoresis of a Bilayer-Coated Silica Bead in an Optical Trap:Application to Enzymology, BIOPHYS. J., 80, 22988-2309 (2001); Assi, F.,Jenks, R., Yang, J., Love, C., Prentiss, M., Massively Parallel Adhesionand Reactivity Measurements Using Simple and Inexpensive MagneticTweezers, J. APPL. PHYS., Vol. 92, No. 9, 5584 (2002); Voldman, J.,Braff, R A., Toner, M., Gray, M. L., Schmidt, M. A., Holding Forces ofSingle-Particle Dielectrophoretic Traps, BIOPHYS. J., 80, 531-541(2001); Huang, H., Dong, H., Sutin, J. D., Kamm, R. D., So, P. T. C.,Three-Dimensional Cellular Deformation Analysis with a Two-PhotonMagnetic Manipulator Workstation, BIOPHYS. J., 82, 2211-2223 (2002),Haber, C., Wirtz, D., Magnetic Tweezers for DNA Micromanipulation, REV.SCI. INSTRUM., Vol. 71, No. 2, 4561 (2000); Hosu, B. G., Jakab, K.,Banki, P., Toth, F. I., Forgacs, G., Magnetic Tweezers for IntracellularApplications, REV. SCI. INSTRUM., Vol. 74, No. 9, 4158 (2003); Smith, S.B., Finzi, L., Bustamante, C., Direct Mechanical Measurements of theElasticity of Single DNA Molecules by Using Magnetic Beads, SCIENCE,Vol. 258, No. 5085, 1122-1126 (1992); all of which are herebyincorporated by reference.

The methods described herein employ various synthetic strategies. Thesestrategies include, but are not limited to: 1) phosphoramidite,phosphodiester, and phosphotriester chemistries, 2) PCR and LCR assemblyschemes, and 3) all biological synthesis schemes using biologicalprotecting groups. These examples are to be considered in all respectsillustrative rather than limiting on the invention described herein.

The methods described herein require a solid-phase support to befunctionalized with only one oligonucleotide in order to havesingle-molecule feedback and error-correction capabilities. In thepreferred embodiment, this monofunctionalization of the solid-phasesupport is performed based on the methods reported by provisionalapplication Ser. No. 10/621,790, titled “Nanoparticle Chains andPreparation Thereof”, filed Jul. 17, 2003 and hereby incorporated byreference.

FIGS. 9A and 9B. Force-feedback using magnetic and optical tweezers.

FIG. 9A. In this scheme, the double-stranded DNA is grown off asolid-phase support by sequential overlapping short DNA strands byannealing partially complementary oligonucleotides, followed byenzymatic ligation. The solid-phase support is a superparamagnetic beadcomprised of a dielectric polymer loaded with superparamagneticnanopoarticles. The support is held in a fixed equilibrium position byapplying an electric field and magnetic field gradient created by themagnetic tweezers that opposes the electrophoretic force. When anoligonucleotide is annealed to the growing strand, the negativelycharged phosphate backbone adds charge to the bead-strand complex.However, the added oligonucleotide adds essentially no mass or surfacearea to the complex. Assuming the zeta-potential of the dielectric beadis constant, the addition of an oligonucleotide strand is the onlycontribution to the increase in electrophoretic force felt by theparticle. The increased electrophoretic force moves the bead from itsequilibrium position, and the magnetic field gradient must be increasedto restore the bead to its equilibrium position. Optically determinedbead velocity and restoration force correspond to the number of basesadded. Therefore, the length of the added strand can be ensured to becorrect. Optical detection can be by way of a CCD or split-photodiode.

FIG. 9B. The scheme in FIG. 9A can also be modified and employ opticaltweezers to apply an optical force rather than a magnetic force. In thisparticular scheme, the optical force can, but need not oppose theelectrophoretic force. The schemes in FIGS. 9A and 9B can be coupledusing magneto-optical tweezers. The optical and magnetic forces can becreated simultaneously or independently of one another.

FIG. 10. Force-feedback systems using only electrophoresis.

DNA ligase- and kinase-mediated single molecule synthesis with feedbackcontrol. In this scheme, a single strand of DNA is synthesized on afluorescent bead functionalized with a single phosphate group, andelectrophoretically passed through a medium with excess ATP, kinase, andligase. The rate of motion of the bead is monitored and used as thefeedback mechanism. There are no protecting groups incorporated in thissynthetic scheme. All synthetic steps employ enzymes. First, excess ATPis passed through the medium simultaneously (with the bead). Excess ATPwill pass through the medium much faster than the bead. The kinase willcatalyze the formation of a triphosphate on the bead using ATP. Whenthis occurs, the rate of motion of the bead will change, due to a changein the charge/mass ratio. The measurement of this change thus serves toindicate a successful reaction. Once the triphosphate has formed on thebead, excess free nucleotide is passed through the medium. These smallmolecules will pass through the medium much faster than the bead. DNAligase will catalyze the addition of the nucleotide, releasing adiphosphate. The rate of motion of the bead is reduced because the lossof the diphosphate decreases the charge/mass ratio. This serves asfeedback for base addition. Multiple-nucleotide addition in this stepshould not occur because after one addition, there is no triphosphatepresent in the system, which DNA ligase needs to add the base. Once asuccessful nucleotide addition is detected, more ATP is introduced intothe system and the described cycle repeats. In one embodiment of thisaspect of the invention, the ligase and kinase activities can belocalized in different regions of the medium, and the bead can be movedback and forth between these regions to allow tighter control over thesynthetic steps.

Heat may also be used as an additional feedback and error correctionmechanism in force feedback systems. For example, the force-feedbacksystems shown in FIGS. 9A-B and 10 can also employ heat as additionalfeedback and error-correction. Prior to enzymatic ligation, the meltingpoint of the small oligonucleotide in contact with the growing nucleicacid strand will be lowered if base-pair mismatches occur. Thecontrolled application of heat after detected annealing can provideadditional feedback about base-pair mismatches. If the oligonucleotidedehybridizes from the growing strand as the melting point is approached,but not reached, a base-pair mismatch is detected when a decrease inmagnetophoretic force, or increase in electrophoretic force is requiredto keep the bead in equilibrium. Because the erroneous strand is removedby heat, this feedback process is also an error-correction mechanism.

Nucleotide removal by exonuclease activity may also be used forerror-correction in force-feedback systems. The schemes in theforce-feedback systems shown in FIGS. 9A-B and 10 may also employnucleotide removal by exonuclease activity as an error-correctionmechanism. This type of error-correction is particular useful forcorrecting errors after enzymatic ligation of an erroneous strand.Whereas it would be extremely difficult to control the exact number ofnucleotides that exonuclease removes from the 3′-end of a growing strandof nucleic acid, that level of control is not required in the methodsreported herein because the feedback systems allow for the length of thestrand to be determined after the error-correction steps. Therefore, iftoo many nucleotides are initially removed, they may be added backlater.

Even though feedback and error-correction at the single-molecule leveltheoretically enables the synthesis of long nucleic acids, one mustaccount for the potential that an error may occur that cannot bedetected or corrected. Therefore, parallelization of single-moleculesystems is desirable to ensure that the process is successful.Furthermore, parallel systems also allows for various nucleic acids ofdifferent sequences to be synthesized simultaneously. For methods andmaterials known in the art related to parallelization methods, see e.g.,Visscher, K., Gross, S. P., Block, S. M., Construction of Multiple-BeamOptical Traps with Nanometer-Resolution Position Sensing, IEEE J.SELECT. TOPICS QUANT. ELECT., Vol. 2, No. 4 (1996), which is herebyincorporated by reference.

FIG. 11A. Parallel single-molecule systems using arrays of light sourcesand detectors. The figure shows an 8×8 array of single-molecule systemsthat are detected using 8×8 arrays of light sources and CCD cameras.

FIG. 11B. Parallel single-molecule systems using one light source anddetector. The figure shows an 8×8 array of single-molecule systems,where each system is as described in FIG. 9B. Only one beam is used asthe illumination source and the trapping laser, and only quadrantphotodiode is used to detect all 64 systems. This is achieved byrastering the laser across all systems using a digital micromirrordevice (DMD). The methods shown in FIG. 11B may be combined with thosein FIG. 8A, where an 8×8 array of single-molecule systems is monitoredusing one light source and an array of quadrant photodiodes asdetectors.

This disclosure also provides for the parallelization of single-moleculesystems without arrays. Single-molecule systems in which the solid-phasesupports have negligible interactions can be parallelized without theuse of arrays.

FIG. 12A. In this scheme, optical tweezers are employed in thesingle-molecule system as described in FIG. 9B. Multiple beads in thesame microscope field of view are trapped by rastering the laser beamusing an acoustical-optical modulator (AOM).

FIG. 12B. In this scheme, multiple beads are tracked using only one CCDcamera. The ability to control beads independently is not available inthis system. However, beads with erroneous nucleic acids can be trackedand discarded after the entire process is complete.

This disclosure also provides methods for the microfabrication ofelectromagnet arrays. The area density of electromagnet arrays ismaximized if the electromagnets are fabricated by bulk-microfabricationtechniques.

FIG. 13A shows a scheme for the microfabrication of quadrupole arrays.First, a layer of diagonal metal wires are lithographically defined anddeposited on a silicon substrate. Bond pads are also defined in thisfirst step. Then, a film of soft magnetic material is lithographicallydesigned and deposited over a portion of the metal lines. A second layerof metal lines are lithographically defined and deposited over themagnetic film layer to complete the microfabrication of in-planemicroelectromagnets.

FIG. 13B shows the cross section of such a microfabricatedelectromagnet.

FIGS. 14A and 14B. Nanopore devices for single-molecule synthesis.

FIG. 14A shows the design of a nanopore device for single-moleculesynthesis with feedback using 5′ protecting groups that may befluorescent. DNA is synthesized on a non-fluorescent solid support andpasses through a channel opening, known in the art as a nanopore, with adetector. The bead can be directed to one of two channels by a switch,depending on whether a successful addition has occurred. After thecoupling step and removal of excess reagents, the bead is passed throughthe pore. The addition can be detected by different means, such as butnot limited to, capacitive measurements (across the channelcorresponding to oligonucleotide length) or fluorescence. For example,fluorescence measurements can be used to detect additions if 5′fluorescent protecting groups are used. A detected increase in lengthcorresponds to a successful addition. If no addition is detected, eitherthe coupling reaction was unsuccessful, or it was successful but notdetected. The bead is directed back into the device for another couplingstep. Because the 5′ end of the growing strand is protected, a redundantcoupling step will not result in multiple-base addition. Once theaddition is successful and detected, the bead is passed into the devicedescribed in FIG. 9B. For methods and materials known in the art relatedto nanopore analysis see, e.g., Deamer, D. W., Branton, D.,Characterization of Nucleic Acids by Nanopore AnalysisI, ACC. CHEM.RES., Vol. 35, No. 10, 817-825 (2002), which is hereby incorporated byreference.

FIG. 14B shows the design of a second nanopore device forsingle-molecule synthesis with feedback using fluorescent 5′ protectinggroups. Monitoring the deprotection of the 5′ group is necessary toeliminate deletion errors. In this device, the growing strand isdeprotected, and the wash is flowed through the nanopore, not the bead,and the nanopore only leads to one channel. If no fluorescence isdetected in the wash, then the strand was not deprotected, or it wassuccessfully deprotected but the fluorescent protecting group was notdetected. The wash is constantly recycled until a fluorescent group isdetected. Because there are no free nucleotides (only the growingstrand) in this device, no addition error can occur by redundant 5′deprotection steps. Once the freed protecting group is detected, thebead is passed back to the device described in FIG. 9A for a subsequentbase addition. Many methods and materials are known in the art relatingto nanopore analysis.

FIGS. 15A-G show an example of the independent control of a cluster ofsuperparamagnetic beads by an electric field and opposing magnetic fieldgradient. These are screenshots obtained from a CCD camera mounted on amicroscope. In each screenshot, the electrophoretic force moves thebeads to the left of the screen, and the magnetic field gradient movesthe bead to the right of the screen (i.e. the positive electrode isoutside and towards the left of the field-of-view, and the magnetictweezer apparatus is outside and towards the right of thefield-of-view).

FIG. 15A. The electric field is on and the magnetic field is off. Thebeads are initially moving to the left because the electrophoretic forceexceeds the magnetophoretic force.

FIG. 15B. The electric field is on and the magnetic field is turned on.The motion of the beads stops because the opposing forces are equal.

FIG. 15C. The magnetic field is increased. The beads move to the rightbecause the magnetophoretic force exceeds the electrophoretic force.

FIG. 15D. The electric field is increased. The motion of the beads stopsbecause the opposing forces are equal.

FIG. 15E. The electric field is further increased. The beads move leftas the electrophoretic force exceeds the magnetophoretic force.

FIGS. 15F and 15G. The experimental system schematic is shown in FIGS.15F and 15G below, and the experimental details can be found in theaccompanying description of FIGS. 15F and 15G. FIGS. 15F and 15G depicta method for the construction of an electrophoretic reservoir andmagnetic tweezer. Superparamagnetic beads 1.05 μm in diameter wereobtained from Dynal Biotech (DynaBeads MyOne Carboxylic Acid). Beadswere washed according to standard protocols and dispersed in distilledwater. The electrode structure was made by thermal evaporation ofaluminum on a glass slide. The electrodes were spaced apart by about 1cm using kapton tape as a mask. The reservoir was created by firstplacing an o-ring between the aluminum pads, and then sealing thereservoir with a glass cover slip. The single-pole magnetic tweezer wasplaced approximately 3 mm from the ground electrode, such that theattractive magnetic field gradient opposed the electrophoretic forcefelt by the beads. The single-pole magnetic tweezer was composed of atip-pole electromagnet with a laser-cut scaffold to bring the tip of thetweezer as close to the top coverslip as possible. The core of theelectromagnet was about 25 mm in length and about 10 mm in diameter. Itwas wrapped about 300 times with insulated copper wire that was pottedusing epoxy. The tips of the electromagnets were cut at about a 45°using a diamond saw. The current through the electromagnet and voltageacross the electrodes were controlled using custom written softwarewritten in Labview. The entire apparatus was placed on the stage of acustom built optical microscope with a 20× condenser lens and 1000×objective lens. Images were collected using a CCD camera and framegrabber that output to the software.

A preferred embodiment of the invention is directed toward the removalof double-stranded oligonucleotides containing sequence mismatch errors.It is particularly related to the removal of error-containingoligonucleotides generated, for example, by chemical or biologicalsynthesis by removing mismatched duplexes using mismatch recognitionproteins. For methods and materials known in the art related to errordetection and correction using mismatch binding proteins, see e.g.,Tabone, et al., WIPO application 03/054232A2 titled Methods for Removalof Double-Stranded Oligonucleotides Containing Sequence Errors UsingMismatch Recognition Proteins, which is hereby incorporated byreference.

FIGS. 16A-C. Removal of error sequences using mismatch binding proteins.An error in a single strand of DNA causes a mismatch in a DNA duplex. Amismatch recognition protein (MMBP), such as a dimer of MutS, binds tothis site on the DNA.

FIG. 16A. A pool of DNA duplexes contains some with mismatches (left)and some which are error-free (right). The 3′-terminus of each DNAstrand is indicated by an arrowhead. An error giving rise to a mismatchis shown as a raised triangular bump on the top left strand. A MMBP isadded and binds selectively to the site of the mismatch. The MMBP-boundDNA duplex is removed, leaving behind a pool which is dramaticallyenriched for error-free duplexes.

FIG. 16B. The DNA-bound protein provides a means to separate theerror-containing DNA from the error-free copies. The protein-DNA complexcan be captured by affinity of the protein for a solid support bearingsuch as a specific antibody, immobilized nickel ions (protein isproduced as a his-tag fusion), streptavidin (protein has been modifiedby the covalent addition of biotin) or by any other such mechanisms asare common to the art of protein purification.

FIG. 16C. Alternatively, the protein-DNA complex is separated from thepool of error-free DNA sequences by a difference in mobility, such as bysize-exclusion column chromatography or by electrophoresis. In thisexample, the electrophoretic mobility in a gel is altered upon MMBPbinding: in the absence of MMBP all duplexes migrate together, but inthe presence of MMBP, mismatch duplexes are retarded (upper band). Themismatch-free band (lower) is then excised and extracted.

FIG. 17. Neutralization of error sequences with mismatch recognitionproteins. The error-containing DNA sequence is not removed from the poolof DNA products. Rather, it becomes irreversibly complexed with amismatch recognition protein by the action of a chemical crosslinkingagent (for example, dimethyl suberimidate, DMS), or of another protein(such as MutL). The pool of DNA sequences is then amplified (such as bythe polymerase chain reaction, PCR), but those containing errors areblocked from amplification, and quickly become outnumbered by theincreasing error-free sequences. As in FIG. 6A, a pool of DNA duplexescontains some DNA duplexes with mismatches (left) and some which areerror-free (right). A MMBP binds selectively to the DNA duplexescontaining mismatches. Application of a crosslinking agent irreversiblyattaches MMBP at the site of the mismatch. Amplification of the pool ofDNA duplexes produces more copies of the error-free duplexes. TheMMBP-mismatch DNA complex is unable to participate in amplificationbecause the bound protein prevents the two strands of the duplex fromdissociating. For long DNA duplexes, the regions outside the MMBP-boundsite may be able to partially dissociate and participate in partialamplification of those (error-free) regions.

As increasingly longer sequences of DNA are generated, the fraction ofsequences which are completely error-free diminishes. At some length, itbecomes likely that there will be no molecule in the entire pool whichcontains a completely correct sequence. Thus, for the generation ofextremely long segments of DNA, it can be useful to produce smallerunits first which can be subjected to the above error controlapproaches. Then these segments can be combined to yield the larger fulllength product. However, if errors in these extremely long sequences canbe corrected locally, without removing or neutralizing the entire longDNA duplex, then the more complex stepwise assembly process can beavoided.

Many biological DNA repair mechanisms rely on recognizing the site of amutation (error) and then using a template strand (most likelyerror-free) to replace the incorrect sequence. In the de novo productionof DNA sequences, this process is complicated by the difficulty ofdetermining which strand contains the error and which should be used asthe template. In this invention, the solutions to this problem rely onusing the pool of other sequences in the mixture to provide the templatefor correction. These methods can be very robust: even if every strandof DNA contains one or more errors, as long as the majority of strandshave the correct sequence at each position (expected because thepositions of errors are generally not correlated between strands), thereis a high likelihood that a given error will be replaced with thecorrect sequence. FIGS. 18, 19, 20A-B, 21A-B, 22, 23A-B, and 24 presentprocedures for performing this sort of local error correction.

Strand-specific error correction. In replicating organisms,enzyme-mediated DNA methylation is often used to identify the template(parent) DNA strand. The newly synthesized (daughter) strand is at firstunmethylated. When a mismatch is detected, the hemimethylated state ofthe duplex DNA is used to direct the mismatch repair system to make acorrection to the daughter strand only. However, in the de novosynthesis of a pair of complementary DNA strands, both strands areunmethylated, and the repair system has no intrinsic basis for choosingwhich strand to correct. In this aspect of the invention, methylationand site-specific demethylation are employed to produce DNA strands thatare selectively hemi-methylated. A methylase, such as the Dam methylaseof E. coli, is used to uniformly methylate all potential target sites oneach strand. The DNA strands are then dissociated, and allowed tore-anneal with new partner strands. A new protein is applied, a fusionof a mismatch binding protein (MMBP) with a demethylase. This fusionprotein binds only to the mismatch, and the proximity of the demethylaseremoves methyl groups from either strand, but only near the site of themismatch. A subsequent cycle of dissociation and annealing allows the(demethylated) error-containing strand to associate with a (methylated)strand which is error-free in this region of its sequence. (This shouldbe true for the majority of the strands, since the locations of errorson complementary strands are not correlated.) The hemi-methylated DNAduplex now contains all the information needed to direct the repair ofthe error, employing the components of a DNA mismatch repair system,such as that of E. coli, which employs MutS, MutL, MutH, and DNApolymerase proteins for this purpose. The process can be repeatedmultiple times to ensure all errors are corrected.

FIG. 18. Two DNA duplexes are shown, identical except for a single baseerror in the top left strand, giving rise to a mismatch. The strands ofthe right hand duplex are shown with thicker lines. Action of amethylase (M) uniformly methylates all possible sites on each DNAstrand. The methylase is removed, and a protein fusion is applied,containing both a mismatch binding protein (MMBP) and a demethylase (D).The MMBP portion of the fusion protein binds to the site of themismatch. Action of the demethylase portion of the fusion proteinremoves methyl groups from both strands in the vicinity of the mismatch.The MMBP-D protein fusion is removed, and the DNA duplexes are allowedto dissociate and re-associate with new partner strands. Theerror-containing strand will most likely re-associate with acomplementary strand which a) does not contain a complementary error atthat site; and b) is methylated near the site of the mismatch. This newduplex now mimics the natural substrate for DNA mismatch repair systems.Application of the components of a mismatch repair system (such as E.coli MutS, MutL, MutH, and DNA polymerase) removes bases in theerror-containing strand (including the error), and uses the opposing(error-free) strand as a template for synthesizing the replacement,leaving a corrected strand.

In a preferred embodiment of the invention, errors are detectable in theform of a DNA mismatch, and can be removed by the combined action of 1)a protein, molecule, or process which recognizes mismatches; and 2) asecond protein, molecucle, or process which cleaves the DNA. FIG. 19illustrates a process for removing errors utilizing a mismatchrecognition function in cooperation with a DNA cleavage agent. FIGS. 20Aand 20B demonstrate one possible design for an agent capable ofcombining these two functions.

Local removal of DNA on both strands at the site of a mismatch ispossible. Various means can be used to create a break in both DNAstrands near an error. For example, a MMBP fusion to a non-specificnuclease (such as DNAseI) can direct the action of the nuclease (N) tothe mismatch site, cleaving both strands. Once the break is generated,homologous recombination can be employed to use other strands (most ofwhich will be error-free at this site) as template to replace theexcised DNA. For example, the RecA protein can be used to facilitatesingle strand invasion, an early step in homologous recombination.Alternatively, a polymerase can be employed to allow broken strands toreassociate with new full-length partner strands, synthesizing new DNAto replace the error.

FIG. 19. Two DNA duplexes are shown, identical except that one containsa single base error as in FIG. 18. A protein, such as a fusion of a MMBPwith a nuclease (N), binds at the site of the mismatch. Alternatively, anuclease with specificity for single-stranded DNA can be employed, usingelevated temperatures to favor local melting of the DNA duplex at thesite of the mismatch. (In the absence of a mismatch, a perfect DNAduplex will be less likely to melt.) Action of an endonuclease, such asthat of the MMBP-N fusion, makes double-stranded breaks near the site ofthe mismatch. The MMBP-N complex is removed, along with the bound shortregion of DNA duplex around the mismatch. Melting and re-annealing ofpartner strands produces some duplexes with single-stranded gaps. A DNApolymerase is used to fill in the gaps, producing DNA duplexes withoutthe original error.

FIGS. 20A and 20B. A protein designed to combine the functions of errorrecognition and error removal. The gene for a mismatch recognitionprotein (such as MutS) has been linked to the gene for a nuclease domain(such as that of restriction endonuclease FokI). when this gene isexpressed, both functions will be combined in the same protein molecule,which will contain two separately folded domains. As MutS forms a dimer,so will this designed protein, allowing it to bind DNA at the site of amismatch and cut both strands of DNA, excising the segment whichcontains an error, as shown in FIG. 19. In a preferred embodiment of theinvention, the designed protein would be thermostable. For example thebinding and nuclease domains could be derived from thermophilicorganisms, or proteins could be engineered for thermostability. Thisfeature would alllow the protein to function in a thermally cycledreaction, such as PCR or LCR, allowing error correction to occur intandem with assembly of molecules of nucleic acid.

FIG. 20A. A designed protein for error recognition and removal. The E.coli mismatch recognition protein MutS and restriction endonuclease FokInuclease domain are used here as an example. These proteins can beproduced as a part of a single polypeptide chain. A linker between thedomains provides the flexibility for both domains to contact the samemolecule(s) of nucleic acid. Additional amino acid sequences can beadded to the design, such as an affinity tag (a Histidine tag is shownhere) used in purification.

FIG. 20B. A single tube process for assembling or amplifying moleculesof nucleic acid while correcting errors. A tube or chamber forthermocycled reactions is divided into two regions, separated by amembrane. As the nucleic acids are assembled (or amplified), athermostable protein (as in FIG. 20A) acts on the nucleic acid to removeerrors. The small pieces of excised error-containing DNA are the onlyones small enough to pass through the membrane to the other side of thechamber. Here they encounter a resin with affinity for nucleic acid, sothat they are not able to pass back into the other chamber, and areeffectively removed from the desired nucleic acid product. Reassembly ofthe nucleic acid molecules surviving this process can be accomplished inmany ways (see FIGS. 19, 21A-B, and 22, and 23A-B), including a PCRreaction which can take place in the same reaction. Multiple thermalcycles dissociate and reassociate the DNA duplexes. Where errors maystill be present, this reassortment of individual strands provides newtemplates for error correction.

FIGS. 21A and 21B follow a process similar to that of FIG. 19. However,in this embodiment of the invention, double-stranded gaps in DNAduplexes are repaired using the protein components of a recombinationrepair pathway. (Note that in this case global melting and re-annealingof DNA strands is not an absolute requirement , which can be preferablewhen dealing with especially large DNA molecules, such as genome lengthDNA.)

FIG. 21A. Two DNA duplexes are shown, identical except that one containsa single base mismatch. A protein, such as a fusion of a MMBP with anuclease (N), is added to bind at the site of the mismatch. Action of anendonuclease, such as that of the MMBP-N fusion, makes double-strandedbreaks around the site of the mismatch. Protein components of a DNArepair pathway, such as the RecBCD complex, are employed to furtherdigest the exposed ends of the double-stranded break, leaving 3′overlaps.

FIG. 21B. Protein components of a DNA repair pathway, such as the RecAprotein, are employed to facilitate single strand invasion of the intactDNA duplex, forming a Holliday junction. A DNA polymerase synthesizesnew DNA, filling in the single-stranded gaps. Protein components of aDNA repair pathway are employed, such as the RuvC protein, to resolvethe Holliday junction(s). The two resulting DNA duplexes do not containthe original error. Note that there can be more than one way to resolvesuch junctions, depending on migration of the branch points.

It is important to make clear that the methods of this invention arecapable of generating large error-free DNA sequences, even if none ofthe initial DNA products are error-free. FIG. 22 summarizes the effectsof the methods of FIG. 19 (or equivalently, FIGS. 21A-B) applied to twoDNA duplexes, each containing a single base (mismatch) error.

FIG. 22. Two DNA duplexes are shown, identical except for a single basemismatch in each, at different locations in the DNA sequence. Mismatchbinding and localized nuclease activity are used to generateddouble-stranded breaks which excise the errors. Recombination repair (asin FIGS. 21A-B) or melting and reassembly (as in FIG. 19) are employedto generate DNA duplexes where each excised error sequence has beenreplaced with newly synthesized sequence, each using the other DNAduplex as template (and unlikely to have an error in that samelocation). Note that complete dissociation and re-annealing of the DNAduplexes is not necessary to generate the error-free products (if themethods shown in FIGS. 21A-B are employed).

A simple way to reduce errors in long DNA molecules is to cleave bothstrands of the DNA backbone at multiple sites, such as with asite-specific endonuclease which generates short single strandedoverhangs at the cleavage site. Of the resulting segments, some areexpected to contain mismatches. These can be removed by the action andsubsequent removal of a mismatch binding protein, as described in FIG.19. The remaining pool of segments can be re-ligated into full lengthsequences. As with the approach of FIGS. 21A-B, this approach includesseveral advantages. 1) loss of an entire full length DNA duplex is notrequired to remove an error; 2) global dissociation and re-annealing ofDNA duplexes is not necessary; 3) error-free DNA molecules can beconstructed from a starting pool in which no one member is an error-freeDNA molecule.

If the most common types of restriction endonucleases were employed forthis approach, all DNA cleavage sites would result in identicaloverhangs. Thus the segments would associate and ligate in random order.However, use of a site-specific “outside cutter” endonuclease (such asHgaI, FokI, or BspMI) produces cleavage sites adjacent to(non-overlapping) the DNA recognition site. Thus each overhang wouldhave sequence specific to that part of the DNA, distinct from that ofthe other sites. The re-association of these specifically complementarycohesive ends will then cause the segments to come together in theproper order. The cohesive ends generated can be up to five bases inlength, allowing for up to 4⁵=1024 different combinations. Conceivablythis many distinct restriction sites could be employed, though the needto avoid near matches between cohesive ends could lower this number.

The necessary restriction sites can be specifically included in thedesign of the sequence, or the random distribution of these sites withina desired sequence can be utilized (the recognition sequence of eachendonuclease allows prediction of the typical distribution of fragmentsproduced). Also, the target sequence can be analyzed for which choice ofendonuclease produces the most ideal set of fragments.

FIGS. 23A and 23B illustrate the semi-selective removal ofmismatch-containing segments.

FIG. 23A. Three DNA duplexes, each containing one error leading to amismatch. DNA is cut with a site-specific endonuclease, leavingdouble-stranded fragments with cohesive ends complementary to theadjacent segment. A MMBP is applied, which binds to each fragmentcontaining a mismatch.

FIG. 23B. Fragments bound to MMBP are removed from the pool, asdescribed in FIGS. 6A and 6B. The cohesive ends of each fragment alloweach DNA duplex to associate with the correct sequence-specific neighborfragment. A ligase (such T4 DNA ligase) is employed to join the cohesiveends, producing full length DNA sequences. These DNA sequences can beerror-free in spite of the fact that none of the original DNA duplexeswas error-free. Incomplete ligation may leave some sequences which areless than full-length, which can be purified away on the basis of size.

According to the invention, the above approaches provide a majoradvantage over one of the conventional methods of removing errors, whichemploys sequencing first to find an error, and then relies on choosingspecific error-free subsequences to “cut and paste” with endonucleaseand ligase. In this embodiment of the invention, no sequencing or userchoice is required in order to remove errors.

When complementary DNA strands are synthesized and allowed to anneal,both strands may contain errors, but the chance of errors occurring atthe same base position in both sequences is extremely small, asdiscussed above. The above methods are useful for eliminating themajority case of uncorrelated errors which can be detected as DNAmismatches. In the rare case of complementary errors at identicalpositions on both strands (undetectable by the mismatch bindingproteins), a subsequent cycle of duplex dissocation and randomre-annealing with a different complementary strand (with a differentdistribution of error positions) remedies the problem. But in someapplications it is desirable to not melt and re-anneal the DNA duplexes,such as in the case of genomic-length DNA strands. This aspect of theinvention reduces correlated errors in such cases. Though the initialpopulation of correlated errors is expected to be low, amplification orother replication of the DNA sequences in a pool will ensure that eacherror is copied to produce a perfectly complementary strand whichcontains the complementary error. According to the invention that thisapproach does not require global dissociation and re-annealing of theDNA strands. Essentially, various forms of DNA damage and recombinationare employed to allow single-stranded portions of the long DNA duplex tore-assort into different duplexes.

FIG. 24 shows a procedure for reducing correlated errors in synthesizedDNA. Two DNA duplexes are shown, identical except for a single error inone strand. Non-specific nucleases are used to generate shortsingle-stranded gaps in random locations in the DNA duplexes in thepool. Shown here is the result of one of these gaps generated at thesite of one of the correlated locations. Recombination-specific proteinssuch as RecA and/or RuvB are employed to mediate the formation of afour-stranded Holliday junction. DNA polymerase is employed to fill inthe gap shown in the lower portion of the complex. Action of otherrecombination and/or repair proteins such as RuvC is employed to cleavethe Holliday junction, resulting in two new DNA duplexes, containingsome sequences which are hybrids of their progenitors. In the exampleshown, one of the error-containing regions has been eliminated. However,since the cutting, rearrangement, and replacement of strands employed inthis method is intended to be random, it is expected that the totalnumber of errors in the sequence will actually not change, simply thaterrors will be reasserted to different strands. Thus, pairs of errorscorrelated in one duplex will be reshuffled into separate duplexes, eachwith a single error. This random reassortment of strands will yield newduplexes containing mismatches which can be repaired using the mismatchrepair proteins detailed above. Unique to this embodiment of theinvention is the use of recombination to separate the correlated errorsinto different DNA duplexes.

As an example application of mismatch repair proteins to DNA errorcontrol, MutS protein (from T. thermophilus, Epicentre) was used toseparate an equal (50/50) mixture of double stranded DNA moleculescontaining both “ideal” homoduplex DNA, and an “error” duplex(mismatched heteroduplex DNA with a single base deletion in one of thestrands). This experiment is shown in FIG. 25. DNA duplexes bound toMutS migrate at a slower rate (upper bands). Even the “ideal” duplexesare bound somewhat by MutS, as expected since the unpurifedoligonucleotides used for this experiment should also contain somefraction of errors. The indicated band was purified from the gel shown,and cloned into the plasmid pCR4blunt-TOPO (Invitrogen). Several ofthese clones (10) were also sequenced. No errors were detected in theseerror-filtered samples (band indicated by a white box in FIG. 25).Unfiltered samples of these duplexes were also cloned and the resultssequenced. Among these samples, errors were found to be common, both thedesigned insertion and other random errors, at an overall frequency of0.57 errors per clone. (The designed insertion was present inapproximately 25% of the DNA stands in the 50/50 mixture.)

FIG. 25. Experimental application of MutS to removal of errors in DNA.Lower arrow: unbound duplexes. Upper arrow: duplexes bound to MutS. Lane1: 20 bp ladder (size standard). Lane 2. 69-mer double stranded DNA (nodesigned mismatches) and MutS protein. Most of the DNA is in the lower(unbound) fraction. Lane 3: 69-mer double stranded DNA (containing asingle base insertion mismatch) and MutS. The unbound 69 bp band isabsent, though a smear is visible above. Lane 4. A 50/50 mixture of thecontents of lanes 2 and 3. Box: this band was excised, purified, andcloned.

The invention may be embodied in other specific forms without departingfrom the spirit or essential characteristics thereof. The foregoingembodiments are therefore to be considered in all respects illustrativerather than limiting on the invention described herein.

1. A method for determining whether a nucleotide or an oligonucleotideis added to a nucleic acid, the method comprising: a) providing a solidsupport having an immobilized nucleic acid; b) performing a nucleic acidaddition reaction by adding a nucleotide or an oligonucleotide to thenucleic acid immobilized on the solid support to synthesize a nucleicacid molecule on the solid support; c) after the nucleic acid additionreaction, passing the solid support through a channel opening with atleast one detector, wherein the at least one detector detects the lengthof a nucleic acid; d) determining whether the nucleotide or theoligonucleotide is added to the nucleic acid immobilized on the solidsupport using the at least one detector, wherein an increase in lengthof the nucleic acid molecule on the solid support indicates that thenucleotide or the oligonucleotide is added to the nucleic acidimmobilized on the solid support; and e) repeating steps b) through d)if the nucleotide or the oligonucleotide is not added to the nucleicacid immobilized on the solid support.
 2. The method of claim 1, whereinthe solid support is a bead or particle and further comprising the stepof detecting whether there is an increase in electrophoretic forceapplied to the solid support when an electric field and a magnetic fieldgradient are applied to the solid support, wherein the increase inelectrophoretic force applied to the solid support is caused by addingthe nucleotide or the oligonucleotide to the nucleic acid immobilized onthe solid support.
 3. A method for determining whether a nucleotide oran oligonucleotide is added to a nucleic acid, the method comprising: a)providing a solid support having an immobilized nucleic acid; b)performing a nucleic acid addition reaction by adding a nucleotidehaving a fluorescent 5′ protecting group or an oligonucleotide having afluorescent 5′ protecting group to the nucleic acid immobilized on thesolid support to synthesize a nucleic acid molecule having a fluorescent5′ protecting group on the solid support; c) after the nucleic acidaddition reaction, passing the solid support through a channel openingwith at least one detector, wherein the at least one detector detectsfluorescent signals; d) determining whether the nucleotide having afluorescent 5′ protecting group or the oligonucleotide having afluorescent 5′ protecting group is added to the nucleic acid immobilizedon the solid support using the at least one detector, wherein thepresence of the nucleic acid molecule having a fluorescent 5′ protectinggroup on the solid support indicates that the nucleotide having afluorescent 5′ protecting group or the oligonucleotide having afluorescent 5′ protecting group is added to the nucleic acid immobilizedon the solid support; and e) repeating steps b) through d) if thenucleotide having a fluorescent 5′ protecting group or theoligonucleotide having a fluorescent 5′ protecting group is not added tothe nucleic acid immobilized on the solid support.
 4. The method ofclaim 3, wherein the solid support is a bead or particle and furthercomprising the step of detecting whether there is an increase inelectrophoretic force applied to the solid support when an electricfield and an magnetic field gradient are applied to the solid support,wherein the increase in electrophoretic force applied to the solidsupport is caused by adding the nucleotide or the oligonucleotide to thenucleic acid immobilized on the solid support.
 5. The method of claim 3,further comprising the steps of: if step d) indicates the presence ofthe nucleic acid molecule having a fluorescent 5′ protecting group onthe solid support, deprotecting the nucleic acid molecule by washing thenucleic acid molecule using a deprotection wash to remove thefluorescent 5′ protecting group of the nucleic acid molecule, andproducing an after-washing solution; flowing the after-washing solutionthrough a channel opening; monitoring the after-washing solution throughthe channel opening for the presence of a removed 5′ protecting group;and repeating the deprotecting, flowing, and monitoring steps if theremoved 5′ protecting group is not detected in the after-washingsolution through the channel opening or adding a nucleotide having a 5′protecting group or an oligonucleotide having a 5′ protecting group tothe nucleic acid molecule on the solid support if the removed 5′protecting group is detected in the after-washing solution through thechannel opening, thereby preventing errors in the sequence of thenucleic acid molecule.
 6. The method of claim 5, wherein the solidsupport is a bead or particle and further comprising the step ofdetecting whether there is an increase in electrophoretic force appliedto the solid support when an electric field and an magnetic fieldgradient are applied to the solid support, wherein the increase inelectrophoretic force applied to the solid support is caused by addingthe nucleotide or the oligonucleotide to the nucleic acid immobilized onthe solid support.
 7. The method of claim 5, wherein the errors in thesequence of the nucleic acid molecule are selected from the groupconsisting of insertion errors, deletion errors, and wrong baseincorporation errors.
 8. The method of claim 5, wherein said monitoringstep is carried out using a plurality of light sources and fluorescencedetectors.
 9. A method for preventing errors in a nucleic acid molecule,the method comprising: a) synthesizing a nucleic acid molecule having a5′ protecting group by adding a nucleotide having a 5′ protecting groupor an oligonucleotide having a 5′ protecting group to a nucleic acid; b)deprotecting the nucleic acid molecule by washing the nucleic acidmolecule using a deprotection wash to remove the 5′ protecting group ofthe nucleic acid molecule, and producing an after-washing solution; c)flowing the after-washing solution through a channel opening andmonitoring the after-washing solution through the channel opening forthe presence of a removed 5′ protecting group; and d) repeating steps b)and c) if the removed 5′ protecting group is not detected in theafter-washing solution through the channel opening or adding anucleotide having a 5′ protecting group or an oligonucleotide having a5′ protecting group to the nucleic acid molecule if the removed 5′protecting group is detected in the after-washing solution through thechannel opening, thereby preventing errors in the sequence of thenucleic acid molecule.
 10. The method of claim 9 wherein the errors inthe sequence of the nucleic acid molecule are selected from the groupconsisting of insertion errors, deletion errors, and wrong baseincorporation errors.
 11. The method of claim 9, wherein the 5′protecting group of the nucleic acid molecule is a fluorescent 5′protecting group and said monitoring step is carried out using aplurality of light sources and fluorescence detectors.